Classifications

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  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7088—Compounds having three or more nucleosides or nucleotides
  • A61K31/7105—Natural ribonucleic acids, i.e. containing only riboses attached to adenine, guanine, cytosine or uracil and having 3'-5' phosphodiester links
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7088—Compounds having three or more nucleosides or nucleotides
  • A61K31/711—Natural deoxyribonucleic acids, i.e. containing only 2'-deoxyriboses attached to adenine, guanine, cytosine or thymine and having 3'-5' phosphodiester links
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
  • A61K48/0058—Nucleic acids adapted for tissue specific expression, e.g. having tissue specific promoters as part of a contruct
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
  • A61P35/02—Antineoplastic agents specific for leukemia
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  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
  • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N2310/00—Structure or type of the nucleic acid
  • C12N2310/10—Type of nucleic acid
  • C12N2310/14—Type of nucleic acid interfering nucleic acids [NA]
  • C12N2310/141—MicroRNAs, miRNAs

Definitions

• the invention relates to compositions, methods, processes, kits and devices for the design, preparation, manufacture and/or formulation of signal-sensor polynucleotides, primary constructs and mRNA molecules for the alteration of cellular phenotypes and micro environments .
• Cancer is a disease characterized by uncontrolled cell division and growth within the body. In the United States, roughly a third of all women and half of all men will experience cancer in their lifetime. Polypeptides are involved in every aspect of the disease including cancer cell biology (carcinogenesis, cell cycle suppression, DNA repair and angiogenesis), treatment (immunotherapy, hormone manipulation, enzymatic inhibition), diagnosis and determination of cancer type (molecular markers for breast, prostate, colon and cervical cancer for example). With the host of undesired
• PCT/US2013/030064 entitled Modified Polynucleotides for the Production of Secreted Proteins
• International Application No PCT/US2013/030059 filed March 9, 2013, entitled Modified Polynucleotides for the Production of Membrane Proteins
• International Application No. PCT/US2013/030066 filed March 9, 2013, entitled Modified Polynucleotides for the Production of Cytoplasmic and Cytoskeletal Proteins
• International Application No. PCT/US2013/030067 filed March 9, 2013, entitled Modified Polynucleotides for the Production of Nuclear Proteins
• International Application No. PCT/US2013/030060 filed March 9, 2013, entitled Modified
• PCT/US2013/030068 filed March 9, 2013, entitled Modified Polynucleotides for the Production of Cosmetic Proteins and Peptides
• International Application No. PCT/US2013/030070 filed March 9, 2013, entitled Modified Polynucleotides for the Production of Oncology-Related Proteins and Peptides
• International Patent Application No. PCT/US2013/031821 filed March 15, 2013, entitled In Vivo Production of Proteins; the contents of each of which are herein incorporated by reference in their entireties.
• next generation of therapeutics must also address the complex cellular microenvironment of the cancer and have the capacity for cell, tissue, organ or patient stratification, whether structurally or functionally.
• nucleic acid based compounds or polynucleotide-encoding nucleic acid-based compounds e.g., signal- sensor polynucleotides
• nucleic acid-based compounds e.g., signal- sensor polynucleotides
• compositions, methods, processes, kits and devices for the design, preparation, manufacture and/or formulation of signal-sensor polynucleotide molecules encoding at least one oncology-related polypeptide of interest may be chemically modified mRNA (mmRNA) molecules.
• mmRNA mRNA
• the present invention provides an isolated signal-sensor polynucleotide comprising a region encoding an oncology-related polypeptide of interest that functions, when translated, to send a death or survival signal.
• death or survival signals include those which (i) alter (increase or decrease) the expression of one or more proteins, nucleic acids, or non-coding nucleic acids, (ii) alter the binding properties of biomolecules within the cell, and/or (iii) perturb the cellular microenvironment in a therapeutically benificial way.
• the signal-sensor polnucleotide may also encode in a flanking region, one or more sensor sequences.
• Such sensor sequences function to "sense" the cell, tissue or ogan microenvironment and confer upon the signal-sensor polynucleotide an altered expression or half life profile (increased or decreased) depending on the interactions of the sensor sequence with the cell, tissue or organ microenvironment.
• signal -sensor polynucleotide comprising, a first region of linked nucleosides, a first flanking region located 5 ' relative to said first region and a second flanking region located 3 ' relative to said first region.
• the first region may encode an oncology-related polypeptide of interest such as, but not limited to, SEQ ID NOs: 1321-2487, 6611-6616 and 7355-7361, 7490, 7492, 7493, 7512, 7514, 7516 and 7517 and the first flanking region may include a sequence of linked nucleosides such as, but not limited to, the native 5' untranslated region (UTR) of any of the nucleic acids that encode any of SEQ ID NOs: 1321-2487, 6611-6616, 7355-7361, 7490, 7492, 7493, 7512, 7514, 7516, 7517, SEQ ID NO: 1-4 and functional variants thereof.
• UTR native 5' untranslated region
• the first region may comprise at least an open reading frame of a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 2488-2496, 6617-6621, 7348-7354, 7362-7489, 7491, 7494, 7506, 7511 and 7513.
• the second flanking region may include a sequence of linked nucleosides such as, but not limited to, the native 3' UTR of any of the nucleic acids that encode any of SEQ ID NOs: 1321-2487, 6611-6616, 7355-7361, 7490, 7492, 7493, 7512, 7514, 7516, 7517, SEQ ID NO: 5-21 and functional variants thereof, and one or more sensor sequences located such as, but not limited to, SEQ ID NOs: 3529-4549, SEQ ID NOs: 5571-6591 and functional variants thereof.
• the signal-sensor polynucleotide may also include a 3' tailing sequence of linked nucleosides.
• a signal-sensor polynucleotide which comprises an mRNA encoding an oncology-related polypeptide of interest and one or more sensor sequences such as, but not limited to, SEQ ID NOs: 3529-4549, SEQ ID NOs: 5571-6591 and functional variants thereof.
• the oncology-related polypeptide of interest may be, but is not limited to, SEQ ID NOs: 1321-2487, 6611-6616, 7355-7361, 7490, 7492, 7493, 7512, 7514, 7516 and 7517.
• the mRNA may include at least one open reading frame of a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 2488-2496, 6617-6621, 7348-7354, 7362-7489, 7491, 7494, 7506, 7511 and 7513.
• the signal-sensor polynucleotides may comprise one, two, three or more than three stop codons.
• the signal-sensor polynucleotides comprise two stop codons.
• the first stop codon is "TGA” and the second stop codon is selected from the group consisting of "TAA,” "TGA” and “TAG.”
• signal-sensor polynucleotides comprise three stop codons.
• the signal-sensor polynucleotides may have a 3 ' tailing sequence of linked nucleosides such as, but not limited to, a poly-A tail of at least 140 nucleotides, a triple helix, and a poly A-G quartet.
• the signal-sensor polynucleotides may have a 5 'cap such as, but not limited to, CapO, Capl, ARC A, inosine, Nl-methyl-guanosine, 2'fluoro-guanosine, 7-deaza- guanosine, 8-oxo-guanosine, 2-amino-guanosine, LNA-guanosine, and 2-azido- guanosine.
• a 5 'cap such as, but not limited to, CapO, Capl, ARC A, inosine, Nl-methyl-guanosine, 2'fluoro-guanosine, 7-deaza- guanosine, 8-oxo-guanosine, 2-amino-guanosine, LNA-guanosine, and 2-azido- guanosine.
• the signal-sensor polynucleotides may include at least one chemical modification such as, but not limited to, modifications located on one or more of a nucleoside and/or the backbone of the nucleotides.
• the signal- sensor polynucleotides comprise a pseudouridine analog such as, but not limited to, 1- carboxymethyl-pseudouridine, 1 -propynyl-pseudouridine, 1 -taurinomethyl- pseudouridine, l-taurinomethyl-4-thio-pseudouridine, 1-methyl-pseudouridine (m ⁇ ), 1- methyl-4-thio-pseudouridine ( sV), 4-thio-l-methyl-pseudouridine, 3-methyl- pseudouridine (m 3 ⁇
• the signal-sensor polynucleotides comprise the pseudouridine analog 1-methylpseudouridine. In yet another embodiment, the signal- sensor polynucleotides comprise the pseudouridine analog 1-methylpseudouridine and the modified nucleoside 5-methylcytidine.
• the signal sensor-polynucleotides may include at least two chemical modifications such as, but not limited to, modifications located on one or more of a nucleoside and/or the backbone of the nucleotides. As a non-limiting example, the signal-sensor polynucleotide comprises the chemical modifications 1- methylpseudouridine and 5-methylcytidine.
• the signal-sensor polynucleotides may comprise at least one translation enhancer element (TEE) such as, but not limited to, TEE-001 - TEE-705.
• TEE translation enhancer element
• the signal-sensor polynucleotide encodes a factor modulating the affinity between HIF subunits and/or HIF-dependent gene expression such as, but not limited to, SEQ ID NO: 6611-6616.
• the signal-sensor polynucleotides may be purified and/or formulated.
• the present invention provides a method of treating a disease, disorder and/or condition in a subject in need thereof by increasing the level of an oncology-related polypeptide of interest comprising administering to said subject an isolated signal-sensor polynucleotide encoding said oncology-related polypeptide.
• the disease, disorder and/or condition may include, but is not limited to, adrenal cortical cancer, advanced cancer, anal cancer, aplastic anemia, bileduct cancer, bladder cancer, bone cancer, bone metastasis, brain tumors, brain cancer, breast cancer, childhood cancer, cancer of unknown primary origin, Castleman disease, cervical cancer, colon/rectal cancer, endometrial cancer, esophagus cancer, Ewing family of tumors, eye cancer, gallbladder cancer, gastrointestinal carcinoid tumors, gastrointestinal stromal tumors, gestational trophoblastic disease, Hodgkin disease, Kaposi sarcoma, renal cell carcinoma, laryngeal and hypopharyngeal cancer, acute lymphocytic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, chronic myelomonocytic leukemia, liver cancer, non-small cell lung cancer, small cell lung cancer, lung carcinoid tumor, lymphoma of the skin
• the present invention provides a method of reducing, eliminating,or preventing tumor growth in a subject in need thereof by increasing the level of an oncology-related polypeptide of interest comprising administering to said subject an isolated signal-sensor polynucleotide encoding said oncology-related polypeptide.
• the tumor growth may be associated with or results from a disease, disorder and/or condition such as, but not limited to, adrenal cortical cancer, advanced cancer, anal cancer, aplastic anemia, bileduct cancer, bladder cancer, bone cancer, bone metastasis, brain tumors, brain cancer, breast cancer, childhood cancer, cancer of unknown primary origin, Castleman disease, cervical cancer, colon/rectal cancer, endometrial cancer, esophagus cancer, Ewing family of tumors, eye cancer, gallbladder cancer, gastrointestinal carcinoid tumors, gastrointestinal stromal tumors, gestational trophoblastic disease, Hodgkin disease, Kaposi sarcoma, renal cell carcinoma, laryngeal and hypopharyngeal cancer, acute lymphocytic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, chronic myelomonocytic leukemia, liver cancer, non-small cell lung cancer, small cell lung cancer, lung carcinoi
• the present invention provides a method of reducing and/or ameliorating at least one symptom of cancer in a subject in need thereof by increasing the level of a polypeptide of interest comprising administering to said subject an isolated signal-sensor polynucleotide encoding said oncology-related polypeptide.
• Non-limiting examples of symptoms include weakness, aches and pains, fever, fatigue, weight loss, blood clots, increased blood calcium levels, low white blood cell count, short of breath, dizziness, headaches, hyperpigmentation, jaundice, erthema, pruritis, excessive hair growth, change in bowel habits, change in bladder function, long-lasting sores, white patches inside the mouth, white spots on the tongue, unusual bleeding or discharge, thickening or lump on parts of the body, indigestion, trouble swallowing, changes in warts or moles, change in new skin and nagging cough and hoarseness.
• the present invention provides a method of preferentially inducing cell death in cancer cells in a tissue or organ comprising contacting the tissue or organ with a signal- sensor polynucleotide encoding an oncology-related polypeptide whose expression triggers apoptosis or cell death and at least one microRNA binding site of a microRNA where the expression of the microRNA in the cancer cell is lower than the expression of the mircroRNA in normal non-cancerous cells.
• the signal-sensor polynucleotide may be administered at a total daily dose of between 0.001 ug and 150 ug.
• Administration of a signal-sensor polynucleotide may be by injection, topical administration, ophthalmic administration or intranasal
• administration may be by injection such as, but not limited to, intradermal, subcutaneous and intramuscular.
• injection such as, but not limited to, intradermal, subcutaneous and intramuscular.
• administration may be topical such as, but not limited to, using creams, lotions, ointments, gels, sprays, solutions and the like.
• FIG. 1 is a schematic of a primary construct of the present invention.
• FIG. 2 is an expanded schematic of the second flanking region of a primary construct of the present invention illustrating the signal-sensor elements of the polynucleotide.
• FIG. 3 is a gel profile of Apoptosis-Inducing Factor short (AIFsh) protein from AIFsh modified mRNA in mammals.
• Figure 3A shows the expected size of AIFsh.
• Figure 3B shows the expected size of AIFsh.
• FIG. 4 is a gel profile of Siah E3 ubiquitin protein ligase 1 (SIAH1) protein from SIAH1 modified mRNA in mammals.
• Figure 4A shows the expected size of SIAH1.
• Figure 4B shows the expected size of SIAH1.
• FIG. 5 is a gel profile of constitutively active (C.A.) caspase 3 (also known as reverse caspase 3 (Rev-Caspase 3)) protein from C.A. caspase 3 modified mRNA in mammals.
• Figure 5 A shows the expected size of C.A. caspase 3.
• Figure 5B shows the expected size of C.A. caspase 3.
• FIG. 6 is a gel profile of Granulysin protein from granulysin modified mRNA in mammals.
• Figure 6A shows the expected size of granulysin.
• Figure 6B shows the expected size of granulysin.
• FIG. 7 is a western blot of C.A. caspase 3 and C.A. caspase 6.
• Figure 7A shows protein from C.A. caspase 3 modified mRNA fully modified with 5-methylcytidine and 1-methylpseudouridine or fully modified with 1-methylpseudouridine.
• Figure 7B shows protein from C.A. caspase 6 modified mRNA fully modified with 5-methylcytidine and 1-methylpseudouridine or fully modified with 1-methylpseudouridine.
• RNA ribonucleic acid
• RNA ribonucleic acid
• compositions including pharmaceutical compositions
• methods for the design, preparation, manufacture and/or formulation of polynucleotides encoding one or more polypeptides of interest are also provided.
• polypeptides of the present invention are encoded by a new class of polynucleotide therapeutics, termed "signal-sensor polynucleotides" which are particularly useful in the stratification, profiling and/or personalization of the signal.
• polynucleotide therapeutice e.g., mRNA
• mRNA polynucleotide therapeutice
• cancer physicochemical environments and metastatic or motility behaviors and according to Hanahan and Weinberg (Cell, 2011, 144:646-674) there are six hallmarks of cancer. These include sustaining a proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis. These hallmarks or functions of cancer allow the cancer to survive, proliferate and disseminate and each arises at different times and in different patterns depending on the cancer type.
• the polynucleotides of the present invention represent such therapeutics; having the ability to selectively stabilize or destabilize cell systems, signal proliferation (survival) or death, trigger the cell cycle or senescence and/or activate or avoid the immune response depending on the cell type, e.g., cancer or normal cell.
• signal-sensor polynucleotide therapeutics may be used to destabilize the survival advantages or hallmarks of a cancer cell (hence they would be cytotoxic).
• diagnostic efforts would include the profiling of the cancer (although this would not be required a priori) including including metabolic state (hypoxic, acidotic), apoptotic vs. survival gene profiles, cell cycle vs. senescent stage, immune status, and stromal factors present.
• the signal-sensor polynucleotide disrupts the transcriptome of the cancer cell.
• the disruption may affect one or more signaling or expression events.
• the encoded oncology-related polypeptide may act upstream of a
• transcription factor known to induce or enhance the expression of genes associated with a cancer. Delivery of the signal-sensor polynucleotide encoding the oncology-related polypeptide which inhibits such a transcription factor (either by binding or sequestration or degradation) would thereby alter the transcriptome of the cancer cell and have a therapeutic benefit.
• One such transcription factor is HIF-1 alpha.
• a signal-sensor polynucleotide encoding a protein which is capable of binding HIF-1 alpha or whose expression results in lower HIF-1 alpha, would effectively turn down HIF-1 alpha regulated genes, e.g., VEGFA or SLC2A1, and destabilize the cancer.
• the profile of the cancer may be evaluated before the signal-sensor polynucleotide is selected.
• profiling data would inform the selection of which oncology-related polypeptide to be delivered.
• the profile of gene expression categorized by hallmark class such as apoptosis, replicative capacity or metabolic signature would allow dynamic instability scoring for a polypeptide and an optimization of therapeutic window for the signal-sensor polynucleotide.
• a "dynamic instability index” refers to a dose of signal-sensor polynuclotide sufficient to induce 50% increase of the oncology-related target protein in vitro in a cancer cell as compared to a normal matched cell.
• Profiling may also be done within hallmark classes such as the distinction between caspase-dependent and caspase independent gene expression for the apoptosis class.
• profiling could be conducted across classes such as gene profiling of apoptosis, senescence (replicative capacity), and metabolic classes.
• the signal-sensor polynucleotides described herein may be used to reduce the expression and/or amount of a polypeptide in a cell.
• MYC inhibitor A, MYC inhibitor B, MYC inhibitor C or MYC inhibitor D may be used on Hep3B cells in order to determine the potentcy of MYC inhibitor A, MYC inhibitor B, MYC inhibitor C or MYC inhibitor D at various concentrations (see e.g., Example 55).
• the signal-sensor polynucleotides described hereim may direct either cytotoxic or cytoprotective therapeutic benefit to specific cells, e.g., normal vs. cancerous.
• signal-sensor polynucleotides would not only encode an oncology-related polypeptide but also a sensor sequence.
• Sensor sequences include, for example, microRNA binding sites, transcription factor binding sites, artificial binding sites engineered to act as pseudo-receptors for endogenous nucleic acid binding molecules.
• a "sensor region” is a region of linked nucleosides of the signal-sensor polynucleotide comprising at least one sensor sequence.
• polynucleotides of the present invention may have one or more sensor regions.
• one or more sensor regions may be located in the first flanking region.
• the sensor region in the first flanking region may comprise at least one sensor sequence.
• the sensor sequence may be, but is not limited to, mir-122, mir-142-3p, mir-142-5p, mir-146, fragments or variants thereof.
• the sensor region in the first flanking region may comprise at least one sensor sequence such as a mir-122 sequence.
• the mir-122 sequence may be, but is not limited to, a mir-122 binding site, mir-122 seed sequence, mir-122 binding site without the seed sequence or a combination thereof.
• one or more sensor regions may be located in the second flanking region.
• the sensor region in the second flanking region may include a sensor sequence such as mir-122, mir-142-3p, mir-142-5p, mir-146, fragments or variants thereof.
• the sensor region in the second flanking region may include three sensor sequences.
• the sensor sequences may be, but are not limited to, mir-122 sequences such as mir-122 binding sites, mir-122 seed sequences, mir-122 binding sites without the seed sequence or a combination thereof.
• the sensor region in the second flanking region is located in the 3 'UTR and the sensor region may include a sensor sequence which is a mir-122 sequence.
• the mir-122 sequence may be, but is not limited to, a mir-122 binding site, mir-122 seed sequence, mir-122 binding site without the seed sequence or a combination thereof.
• two or more sensor regions may be located in the same region of the signal-sensor polynucleotide such as, but not limited to, a first region first region of linked nucleotides, the first flanking region and/or the second flanking region.
• the two or more sensor regions are located in the second flanking region.
• three sensor regions are located in the 3' UTR in the second flanking region.
• the three sensor regions may include, mir-122 binding sites, mir-122 seed sequences, mir-122 binding sites without the seed sequence or a combination thereof
• two or more sensor regions may be located in different regions of the signal-sensor polynucleotide such as, but not limited to, the first region of linked nucleotides, the first flanking region and/or the second flanking region.
• a first sensor region is located in the first flanking region and a second sensor region is located in the second flanking region.
• the sensor regions may comprise the same sensor sequence or different sensor sequences.
• a start codon is located within a sensor region.
• a sensor region may comprise two or more sensor sequences.
• the sensor sequences may be the same or different.
• the sensor region may comprise two or more sensor sequence which are different from each other but they may be based on the same mir binding site.
• the sensor region may include at least one miR binding site sequence and at least one mir binding site sequence with the seed removed.
• the sensor region may include at least one miR binding site sequence and at least one miR seed sequence.
• the sensor region may include at least one miR binding site sequence with the seed removed and at least one miR seed sequence.
• the sensor region may comprise two or more sensor sequences which are in a pattern such as ABABAB or AABBAABBAABB or
• each letter, A, B, or C represent a different miR sequence.
• the signal-sensor polynucleotide may include two or more sensor regions with each sensor region having one or more sensor sequences.
• the sensor 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 sensor regions.
• the sensor sequences may be in a pattern such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than three times across the entire signal-sensor polynucleotide.
• each letter, A, B, or C represent a different miR sequence.
• the first sensor region may have sensor sequences in the pattern ABA and the second sensor region may have sensor sequences in the pattern BAB so the overall pattern of the sensor sequences in the signal- sensor polynucleotide is ABABAB.
• the first sensor region may have sensor sequences AA
• the second sensor region may have sensor sequences BB
• the third sensor region may have sensor sequences AA
• the fourth sensor region may have sensor seuqences BB so the overall pattern of the sensor sequences in the signal-sensor polynucleotide is AABBAABB.
• the sensor sequences in the signal-sensor polynucleotides of the present invention may include one or more regulatory sequences in the 3-UTR and/or 5'UTR of natural mRNAs, which regulate mRNA stability and translation in different tissues and cells.
• Such cis-regulatory elements may include, but are not limited to, Cis- RNP
• CDEs are a class of regulatory motifs that mediate mRNA degradation through their interaction with Roquin proteins.
• CDEs are found in many mRNAs that encode regulators of development and inflammation to limit cytokine production in macrophage (Leppek K et al, Cell, 2013, 153, 869-881, which is herein incorporated by reference in its entirety.).
• a particular CDE can be introduced to the signal-sensor polynucleotide when the degradation of polypeptides in a cell or tissue is desired.
• a particular CDE can also be removed from the signal-sensor polynucleotide in order to maintain a more stable mRNA in a cell or tissue for sustaining protein expression.
• microRNA profiling of the cancer cells or tissues may be conducted to determine the presence or absence of miRNA in the cells or tissues to determine the appropriate microRNA to use as sensor sequences in the signal sensor polynucleotides.
• MicroRNA gene regulation may be influenced by the sequence surrounding the microRNA such as, but not limited to, the species of the surrounding sequence, the type of sequence (e.g., heterologous, homologous and artificial), regulatory elements in the surrounding sequence and/or structural elements in the surrounding sequence.
• the microRNA may be influenced by the 5 'UTR and/or the 3 'UTR.
• a non-human 3 'UTR may increase the regulatory effect of the microRNA sequence on the expression of a polypeptide of interest compared to a human 3 'UTR of the same sequence type.
• Other regulatory elements and/or structural elements of the 5' -UTR can influence microRNA mediated gene regulation.
• One such example is a structured IRES (Internal Ribosome Entry Site) in the 5 'UTR, which is necessary for the binding of translational elongation factors to initiate protein translation. EIF4A2 binding to this secondarily structured element in the 5 'UTR is necessary for microRNA mediated gene expression (Meijer HA et al, Science, 2013, 340, 82-85, herein incorporated by reference in its entirety).
• the sensor-signal polynucleotide can further be modified to include this structured 5' -UTR in order to enhance microRNA mediated gene regulation.
• At least one microRNA site can be engineered into the 3' UTR of the signal- sensor polynucleotides of the present invention.
• at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten or more microRNA sites may be engineered into the 3 ' UTR of the signal-sensor polynucleotides of the present invention.
• the microRNA sites incorporated into the signal-sensor polynucleotides may be the same or may be different microRNA sites.
• the microRNA sites incorporated into the signal-sensor polynucleotides may target the same or different tissues in the body.
• tissue-, cell-type-,or disease-specific microRNA binding sites in the 3 ' UTR of a signal-sensor polynucleotide can be reduced.
• tissue-, cell-type-,or disease-specific microRNA binding sites in the 3 ' UTR of a signal-sensor polynucleotide e.g. hepatocytes, myeloid cells, endothelial cells, cancer cells, etc.
• a microRNA site can be engineered near the 5 ' terminus of the 3 'UTR, about halfway between the 5' terminus and 3 'terminus of the 3 'UTR and/or near the 3 'terminus of the 3 'UTR.
• a microRNA site may be engineered near the 5' terminus of the 3 'UTR and about halfway between the 5' terminus and 3 'terminus of the 3 'UTR.
• a microRNA site may be engineered near the 3 'terminus of the 3 'UTR and about halfway between the 5' terminus and 3 'terminus of the 3'UTR.
• a microRNA site may be engineered near the 5' terminus of the 3'UTR and near the 3' terminus of the 3'UTR.
• a 3'UTR can comprise 4 microRNA sites.
• the microRNA sites may be complete microRNA binding sites, microRNA seed sequences and/or microRNA binding site sequences without the seed sequence.
• a signal-sensor polynucleotide may be engineered to include microRNA sites which are expressed in different tissues of a subject.
• a signal-sensor polynucleotide of the present invention may be engineered to include miR-192 and miR-122 to regulate expression of the signal-sensor polynucleotide in the liver and kidneys of a subject.
• a signal- sensor polynucleotide may be engineered to include more than one microRNA sites for the same tissue.
• a signal-sensor polynucleotide of the present invention may be engineered to include miR- 17-92 and miR-126 to regulate expression of the signal- sensor polynucleotide in endothelial cells of a subject.
• the therapeutic window and or differential expression associated with the oncology-related polypeptide encoded by the signal-sensor polynucleotide of the invention may be altered.
• polynucleotides may be designed whereby a death signal is more highly expressed in cancer cells (or a survival signal in a normal cell) by virtue of the miRNA signature of those cells.
• a cancer cell expresses a lower level of a particular miRNA
• the signal-sensor polynucleotide encoding the binding site for that miRNA (or miRNAs) would be more highly expressed.
• the oncology-related polypeptide encoded by the signal-sensor polynucleotide is selected as a protein which triggers or induces cell death.
• Neigboring noncancer cells harboring a higher expression of the same miRNA would be less affected by the encoded death signal as the signal-sensor polynucleotide would be expressed at a lower level due to the affects of the miRNA binding to the binding site or "sensor" encoded in the 3'UTR. Conversely, cell survival or
• cytoprotective signals may be delivered to tissues containing cancer and non cancerous cells where a miRNA has a higher expression in the cancer cells— the result being a lower survival signal to the cancer cell and a larger survival signature to the normal cell.
• Multiple signal-sensor polynucleotides may be designed and administered having different signals according to the previous paradigm.
• the expression of a signal-sensor polynucleotide may be controlled by incorporating at least one sensor sequence in the signal-sensor
• a polynucleotide may be targeted to an orthotopic tumor by having a polynucleotide incorporating a miR-122 binding site and formulated in a lipid
• nanoparticle comprising the cationic lipid DLin-KC2-DMA (see e.g., the experiments described in Example 56A and 56B).
• signal-sensor polynucleotides can be engineered for more targeted expression in specific cell types or only under specific biological conditions.
• signal-sensor polynucleotides could be designed that would be optimal for protein expression in a tissue or in the context of a biological condition such as cancer.
• Transfection experiments can be conducted in relevant cell lines, using engineered signal-sensor polynucleotides and protein production can be assayed at various time points post-transfection.
• cells can be transfected with different microRNA binding site-engineering nucleic acids or signal-sensor polynucleotides and by using an ELISA kit to the relevant protein and assaying protein produced at 6 hr, 12 hr, 24 hr, 48 hr, 72 hr and 7 days post-transfection.
• In vivo experiments can also be conducted using microRNA-binding site-engineered molecules to examine changes in tissue-specific expression of formulated signal-sensor polynucleotides.
• the signal-sensor polynucleotides of the invention may include at least one microRNA in order to dampen the antigen presentation by antigen presenting cells.
• the microRNA may be the complete microRNA sequence, the microRNA seed sequence, the microRNA sequence without the seed or a combination thereof.
• the microRNA incorporated into the signal-sensor polynucleotide may be specific to the hematopoietic system.
• the microRNA incorporated into the signal-sensor polynucleotides of the invention to dampen antigen presentation is miR-142-3p.
• the signal-sensor polynucleotides of the invention may include at least one microRNA in order to dampen expression of the encoded polypeptide in a cell of interest.
• the signal-sensor polynucleotides of the invention may include at least one miR-122 binding site in order to dampen expression of an encoded polypeptide of interest in the liver.
• the signal-sensor polynucleotides of the invention may include at least one miR-142-3p binding site, miR-142-3p seed sequence, miR-142-3p binding site without the seed, miR- 142-5p binding site, miR-142-5p seed sequence, miR-142-5p binding site without the seed, miR-146 binding site, miR-146 seed sequence and/or miR-146 binding site without the seed sequence (see e.g., the experiment outlined in Example 47 and Example 60).
• the signal-sensor polynucleotides described herein may be modified as to avoid the deficiencies of other polypeptide-encoding molecules of the art.
• the signal-sensor polynucleotides are referred to as modified signal-sensor polynucleotides or primary constructs, modified mRNA or mmRNA.
• signal-sensor polynucleotide polynucleotides, primary constructs and/or mmRNA encoding oncology-related polypeptides of interest which have been designed to improve one or more of the stability and/or clearance in tissues, receptor uptake and/or kinetics, cellular access by the compositions, engagement with translational machinery, mRNA half-life, translation efficiency, immune evasion, protein production capacity, secretion efficiency (when applicable), accessibility to circulation, protein half-life and/or modulation of a cell's status, function and/or activity.
• the present invention provides nucleic acid molecules, specifically signal- sensor polynucleotides, primary constructs and/or mmRNA which encode one or more oncology-related polypeptides of interest. Specifically the invention contemplates signal- sensor polynucleotides which are useful in cancer or cancer related diseases, disorders.
• signal-sensor polynucleotides are nucleic acid transcripts which encode one or more oncology-related polypeptides of interest that, when translated, delivers a "signal" to the cell (cancer or noncancerous) which results in the therapeutic benefit to the organism of either being detrimental to the cancer cell or beneficial to normal cells or both detrimental to cancer cells and advantageous to normal cells.
• the signal-sensor polynucleotides may optionally further comprise a sequence (translatable or not) which "senses" the microenvironment of the polynucleotide and alters (a) the function or phenotypic outcome associated with the peptide or protein which is translated, (b) the expression level of the signal-sensor polynucleotide, and/or both.
• nucleic acid in its broadest sense, includes any compound and/or substance that comprise a polymer of nucleotides. These polymers are often referred to as polynucleotides.
• Exemplary 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 de
• the signal-sensor polynucleotide or nucleic acid molecule is 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.
• Signal-sensor polynucleotides of the invention may be mRNA or any nucleic acid molecule and may or may not be chemically modified.
• 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 signal-sensor polynucleotides or primary RNA 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 including, in some embodiments, the lack of a substantial induction of the innate immune response of a cell into which the signal-sensor polynucleotide is introduced.
• modified mRNA molecules of the present invention which may be synthetic, are termed "mmRNA.”
• mmRNA a "structural" feature or modification is one in which two or more linked nucleotides are inserted, deleted, duplicated, inverted or randomized in a signal-sensor polynucleotide polynucleotide, primary construct or mmRNA without significant chemical modification to the nucleotides themselves.
• the polynucleotide "ATCG” may be chemically modified to "AT-5meC-G".
• the same polynucleotide may be structurally modified from "ATCG” to "ATCCCG”.
• the dinucleotide "CC” has been inserted, resulting in a structural modification to the polynucleotide.
• the signal-sensor polynucleotides of the present invention are distinguished from wild type mRNA in their functional and/or structural design features which serve to, as evidenced herein, overcome existing problems of effective polypeptide production using nucleic acid-based therapeutics.
• Figure 1 shows a representative signal-sensor primary construct 100 of the present invention.
• the term "primary construct” or “primary mRNA construct” refers to a signal-sensor polynucleotide transcript which encodes one or more polypeptides of interest and which retains sufficient structural and/or chemical features to allow the polypeptide of interest encoded therein to be translated.
• Signal-sensor primary constructs may be polynucleotides of the invention. When structurally or chemically modified, the signal-sensor primary construct may be referred to as a mmRNA.
• the primary construct 100 here contains a first region of linked nucleotides 102 that is flanked by a first flanking region 104 and a second flaking region 106.
• the "first region” may be referred to as a "coding region” or “region encoding” or simply the “first region.”
• This first region may include, but is not limited to, the encoded oncology-related polypeptide of interest.
• the oncology-related polypeptide of interest may comprise at its 5 ' terminus one or more signal peptide sequences encoded by a signal peptide sequence region 103.
• the flanking region 104 may comprise a region of linked nucleotides comprising one or more complete or incomplete 5' UTRs sequences.
• the flanking region 104 may also comprise a 5' terminal cap 108.
• the second flanking region 106 may comprise a region of linked nucleotides comprising one or more complete or incomplete 3' UTRs.
• the flanking region 106 may also comprise a 3' tailing sequence 110 and a 3'UTR 120.
• first operational region 105 Bridging the 5' terminus of the first region 102 and the first flanking region 104 is a first operational region 105.
• this operational region comprises a start codon.
• the operational region may alternatively comprise any translation initiation sequence or signal including a start codon.
• this operational region comprises a stop codon.
• the operational region may alternatively comprise any translation initiation sequence or signal including a stop codon. According to the present invention, multiple serial stop codons may also be used.
• the operation region of the present invention may comprise two stop codons.
• the first stop codon may be "TGA” and the second stop codon may be selected from the group consisting of "TAA,” “TGA” and “TAG.”
• the operation region may further comprise three stop codons.
• the third stop codon may be selected from the group consisting of "TAA,” “TGA” and "TAG.”
• the 3'UTR 120 of the second flanking region 106 may comprise one or more sensor sequences 130.
• a region comprising at least one sensor sequence is referred to as a "sensor region.”
• These sensor sequences as discussed herein operate as pseudo-receptors (or binding sites) for ligands of the local microenvironment of the primary construct or signal-sensor polynucleotide.
• microRNA bindng sites or miRNA seeds may be used as sensors such that they function as pseudoreceptors for any microRNAs present in the environment of the polynucleotide.
• the shortest length of the first region of the signal-sensor primary construct of the present invention can be the length of a nucleic acid sequence that is sufficient to encode for a dipeptide, a tripeptide, a tetrapeptide, a pentapeptide, a hexapeptide, a heptapeptide, an octapeptide, a nonapeptide, or a decapeptide.
• the length may be sufficient to encode a peptide of 2-30 amino acids, e.g. 5- 30, 10-30, 2-25, 5-25, 10-25, or 10-20 amino acids.
• the length may be sufficient to encode for a peptide of at least 11, 12, 13, 14, 15, 17, 20, 25 or 30 amino acids, or a peptide that is no longer than 40 amino acids, e.g. no longer than 35, 30, 25, 20, 17, 15, 14, 13, 12, 11 or 10 amino acids.
• the length of the first region encoding the oncology-related polypeptide of interest of the present invention is greater than about 30 nucleotides in length (e.g., at least or greater than about 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, 1,000, 1,100, 1,200, 1,300, 1,400, 1,500, 1,600, 1,700, 1,800, 1,900, 2,000, 2,500, and 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 20,000, 30,000, 40,000, 50,000, 60,000, 70,000, 80,000, 90,000 or up to and including 100,000 nucleotides).
• the "first region” may be referred to as a "coding region” or "region encoding” or simply the "first region.”
• the signal-sensor polynucleotide polynucleotide, primary construct, or mmRNA includes 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 100,000,
• nucleotides
• the first and second flanking regions may range independently from 15-1,000 nucleotides in length (e.g., greater than 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 30, 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).
• 15-1,000 nucleotides in length e.g., greater than 30, 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.
• the tailing sequence may range from absent to 500 nucleotides in length (e.g., at least 60, 70, 80, 90, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, or 500 nucleotides).
• the length may be determined in units of or as a function of polyA binding protein binding.
• the polyA tail is long enough to bind at least 4 monomers of polyA binding protein.
• PolyA binding protein monomers bind to stretches of approximately 38 nucleotides. As such, it has been observed that polyA tails of about 80 nucleotides and 160 nucleotides are functional.
• the capping region may comprise a single cap or a series of nucleotides forming the cap.
• the capping region may be from 1 to 10, e.g. 2-9, 3-8, 4-7, 1-5, 5-10, or at least 2, or 10 or fewer nucleotides in length.
• the cap is absent.
• the first and second operational regions may range from 3 to 40, e.g., 5-30, 10-20, 15, or at least 4, or 30 or fewer nucleotides in length and may comprise, in addition to a start and/or stop codon, one or more signal and/or restriction sequences.
• a signal-sensor primary construct or mmR A may be cyclized, or concatemerized, to generate a translation competent molecule to assist interactions between poly- A binding proteins and 5 '-end binding proteins.
• the mechanism of cyclization or concatemerization may occur through at least 3 different routes: 1) chemical, 2) enzymatic, and 3) ribozyme catalyzed.
• the newly formed 5'-/3'-linkage may be intramolecular or intermolecular.
• the 5 '-end and the 3 '-end of the nucleic acid may contain chemically reactive groups that, when close together, form a new covalent linkage between the 5 '-end and the 3 '-end of the molecule.
• the 5 '-end may contain an NHS-ester reactive group and the 3 '-end may contain a 3'-amino-terminated nucleotide such that in an organic solvent the 3'-amino-terminated nucleotide on the 3 '-end of a synthetic mRNA molecule will undergo a nucleophilic attack on the 5'-NHS-ester moiety forming a new 5 '-/3 '-amide bond.
• T4 RNA ligase may be used to enzymatically link a 5'- phosphorylated nucleic acid molecule to the 3'-hydroxyl group of a nucleic acid forming a new phosphorodiester linkage.
• ⁇ g of a nucleic acid molecule is incubated at 37°C for 1 hour with 1-10 units of T4 RNA ligase (New England Biolabs, Ipswich, MA) according to the manufacturer's protocol.
• the ligation reaction may occur in the presence of a split oligonucleotide capable of base-pairing with both the 5'- and 3'- region in juxtaposition to assist the enzymatic ligation reaction.
• either the 5 '-or 3 '-end of the cDNA template encodes a ligase ribozyme sequence such that during in vitro transcription, the resultant nucleic acid molecule can contain an active ribozyme sequence capable of ligating the 5 '-end of a nucleic acid molecule to the 3 '-end of a nucleic acid molecule.
• the ligase ribozyme may be derived from the Group I Intron, Group I Intron, Hepatitis Delta Virus, Hairpin ribozyme or may be selected by SELEX (systematic evolution of ligands by exponential enrichment).
• the ribozyme ligase reaction may take 1 to 24 hours at temperatures between 0 and 37°C.
• polynucleotides, primary constructs or mmRNA 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.
• the glyoxylate cycle enzymes, isocitrate lyase and malate synthase may be supplied into HepG2 cells at a 1 : 1 ratio to alter cellular fatty acid metabolism.
• This ratio may be controlled by chemically linking signal-sensor polynucleotides, primary constructs or mmRNA using a 3'-azido terminated nucleotide on one signal-sensor polynucleotide, primary construct or mmRNA species and a C5-ethynyl or alkynyl-containing nucleotide on the opposite signal-sensor polynucleotide, primary construct or mmRNA species.
• the modified nucleotide is added post-transcriptionally using terminal transferase (New England Biolabs, Ipswich, MA) according to the manufacturer's protocol.
• the two signal-sensor polynucleotide, primary construct or mmR A species may be combined in an aqueous solution, in the presence or absence of copper, to form a new covalent linkage via a click chemistry mechanism as described in the literature.
• more than two signal-sensor polynucleotides may be linked together using a functionalized linker molecule.
• a functionalized saccharide molecule may be chemically modified to contain multiple chemical reactive groups (SH-, NH 2 -, N 3 , etc...) to react with the cognate moiety on a 3 '-functionalized signal-sensorpolynucleotide molecule (i.e., a 3'-maleimide ester, 3'-NHS-ester, alkynyl).
• the number of reactive groups on the modified saccharide can be controlled in a stoichiometric fashion to directly control the stoichiometric ratio of conjugated signal- sensor polynucleotide, primary construct or mmRNA.
• signal-sensor polynucleotide primary constructs or mmRNA of the present invention can be designed to be conjugated to other polynucleotides, oncology-related polypeptides, 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.
• alkylating agents phosphate, amino, mercapto, PEG ⁇ e.g., PEG-40K
• MPEG MPEG
• [MPEG] 2 polyamino, alkyl, substituted alkyl, radiolabeled markers, enzymes, haptens ⁇ e.g. biotin)
• 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.
• proteins e.g., glycoproteins, or peptides, e.g., molecules having a specific affinity for a co-ligand
• 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.
• Conjugation may result in increased stability and/or half life and may be particularly useful in targeting the signal-sensor polynucleotides, primary constructs or mmRNA to specific sites in the cell, tissue or organism.
• the signal-sensor polynucleotide mmRNA or primary constructs may be administered with, or further encode one or more of RNAi agents, siRNAs, shRNAs, miRNAs, miRNA binding sites, antisense RNAs, ribozymes, catalytic DNA, tRNA, RNAs that induce triple helix formation, aptamers or vectors, and the like.
• RNAi agents siRNAs, shRNAs, miRNAs, miRNA binding sites, antisense RNAs, ribozymes, catalytic DNA, tRNA, RNAs that induce triple helix formation, aptamers or vectors, and the like.
• the signal-sensor polynucleotides described herein may be conjugated with a moiety to target various cancer cells such as, but not limited to, the moieties described in US Patent Application No. US20130216561, the contents of which are herein incorporated by reference in its entirety.
• the linkage between the signal- sensor polynucleotides and the cancer targeting moiety may be an acid cleavable linkage that can increase the efficacy of the conjugate such as, but not limited to, the linkages described in US Patent Application No. US20130216561, the contents of which are herein incorporated by reference in its entirety.
• bifunctional signal-sensor polynucleotides are those having or capable of at least two functions. These molecules may also by convention be referred to as multifunctional.
• bifunctional signal-sensor polynucleotides may be encoded by the RNA (the function may not manifest until the encoded product is translated) or may be a property of the polynucleotide itself. It may be structural or chemical.
• Bifunctional modified signal-sensor polynucleotides may comprise a function that is covalently or electrostatically associated with the polynucleotides. Further, the two functions may be provided in the context of a complex of a signal-sensor polynucleotide and another molecule.
• Bifunctional signal-sensor polynucleotides may encode oncology-related peptides which are anti-proliferative. These peptides may be linear, cyclic, constrained or random coil. They may function as aptamers, signaling molecules, ligands or mimics or mimetics thereof. Anti-proliferative peptides may, as translated, be from 3 to 50 amino acids in length. They may be 5-40, 10-30, or approximately 15 amino acids long. They may be single chain, multichain or branched and may form complexes, aggregates or any multi-unit structure once translated.
• Noncoding Signal-Sensor Polynucleotides As described herein, provided are signal-sensor polynucleotides and primary constructs having sequences that are partially or substantially not translatable, e.g., having a noncoding region.
• Such noncoding region may be the "first region" of the signal-sensor primary construct.
• the noncoding region may be a region other than the first region.
• Such molecules are generally not translated, but can exert an effect on protein production by one or more of binding to and sequestering one or more translational machinery components such as a ribosomal protein or a transfer R A (tRNA), thereby effectively reducing protein expression in the cell or modulating one or more pathways or cascades in a cell which in turn alters protein levels.
• tRNA transfer R A
• the signal-sensor polynucleotide and/or primary construct may contain or encode one or more long noncoding RNA (IncRNA, or lincRNA) or portion thereof, a small nucleolar RNA (sno- RNA), micro RNA (miRNA), small interfering RNA (siRNA) or Piwi-interacting RNA (piRNA).
• RNA long noncoding RNA
• miRNA micro RNA
• siRNA small interfering RNA
• piRNA Piwi-interacting RNA
• the signal-sensor polynucleotides of the present invention may be auxotrophic.
• auxotrophic refers to signal-sensor polynucleotides that comprise at least one feature that triggers, facilitates or induces the degradation or inactivation of the itself in response to spatial or temporal cues such that oncology-related protein expression is substantially prevented or reduced.
• spatial or temporal cues include the location of the signal-sensor polynucleotide to be translated such as a particular tissue or organ or cellular environment. Also contemplated are cues involving temperature, pH, ionic strength, moisture content, and the like.
• the feature is located in a terminal region of the signal- sensor polynucleotides of the present invention.
• the auxotrophic mRNA may contain a miR binding site in the terminal region which binds to a miR expressed in a selected tissue so that the expression of the auxotrophic mRNA is substantially prevented or reduced in the selected tissue.
• an auxotrophic mRNA containing a miR- 122 binding site will not produce protein if localized to the liver since miR- 122 is expressed in the liver and binding of the miR would effectuate destruction of the auxotrophic mRNA.
• HEK293 cells do not express miR- 122 so there would be little to no downregulation of a signal-sensor polynucleotide having a miR-122 sequence in HEK293 but for hepatocytes which do expression miR-122 there would be a downregulation of a signal-sensor polynucleotide having a miR-122 sequence in hepatocytes (see e.g., the study outlined Example 19).
• the miR-122 level can be measured in HeLa cells, primary human hepatocytes and primary rat hepatocytes prior to
• a signal-sensor polynucleotide encoding having at least one miR-122 binding site, miR-122 binding site without the seed sequence or a miR-122 binding site After administration the expression of the signal-sensor polynucleotide can be measured to determine the dampening effect of the miR-122 in the signal-sensor polynucleotide (see e.g., the studies outlined in Examples 41, 42, 43 57, 58 and 59).
• the effectiveness of the miR-122 binding site, miR-122 seed or the miR-122 binding site without the seed in different 3'UTRs may be evaluated in order to determine the proper UTR for the desired outcome such as, but not limited to, the highest dampening effect (see e.g., the study outlined in Example 46).
• the degradation or inactivation of auxotrophic mRNA may comprise a feature responsive to a change in pH.
• the auxotrophic mRNA may be triggered in an environment having a pH of between pH 4.5 to 8.0 such as at a pH of 5.0 to 6.0 or a pH of 6.0 to 6.5.
• the change in pH may be a change of 0.1 unit, 0.2 units, 0.3 units, 0.4 units, 0.5 units, 0.6 units, 0.7 units, 0.8 units, 0.9 units, 1.0 units, 1.1 units, 1.2 units, 1.3 units, 1.4 units, 1.5 units, 1.6 units, 1.7 units, 1.8 units, 1.9 units, 2.0 units, 2.1 units, 2.2 units, 2.3 units, 2.4 units, 2.5 units, 2.6 units, 2.7 units, 2.8 units, 2.9 units, 3.0 units, 3.1 units, 3.2 units, 3.3 units, 3.4 units, 3.5 units, 3.6 units, 3.7 units, 3.8 units, 3.9 units, 4.0 units or more.
• the degradation or inactivation of auxotrophic mRNA may be triggered or induced by changes in temperature.
• a change of temperature from room temperature to body temperature may be less than 1°C, less than 5°C, less than 10°C, less than 15°C, less than 20°C, less than 25°C or more than 25°C.
• the degradation or inactivation of auxotrophic mRNA may be triggered or induced by a change in the levels of ions in the subject.
• the ions may be cations or anions such as, but not limited to, sodium ions, potassium ions, chloride ions, calcium ions, magnesium ions and/or phosphate ions.
• the signal-sensor primary construct is designed to encode one or more oncology-related polypeptides of interest or fragments thereof.
• An oncology-related polypeptide of interest may include, but is not limited to, whole polypeptides, a plurality of polypeptides or fragments of polypeptides, which independently may be encoded by one or more nucleic acids, a plurality of nucleic acids, fragments of nucleic acids or variants of any of the aforementioned.
• the term "oncology-related polypeptides of interest” refers to any polypeptide which is selected to be encoded in the signal-sensor primary construct of the present invention.
• polypeptide means a polymer of amino acid residues (natural or unnatural) linked together most often by peptide bonds.
• polypeptides include gene products, naturally occurring polypeptides, synthetic polypeptides, homologs, orthologs, paralogs, fragments and other equivalents, variants, and analogs of the foregoing.
• a polypeptide may be a single molecule or may be a multi-molecular complex such as a dimer, trimer or tetramer. They may also comprise single chain or multichain polypeptides such as antibodies or insulin and may be associated or linked. Most commonly disulfide linkages are found in multichain polypeptides.
• the term polypeptide may also apply to amino acid polymers in which one or more amino acid residues are an artificial chemical analogue of a corresponding naturally occurring amino acid.
• polypeptide variant refers to molecules which differ in their amino acid sequence from a native or reference sequence.
• the amino acid sequence variants may possess substitutions, deletions, and/or insertions at certain positions within the amino acid sequence, as compared to a native or reference sequence.
• variants will possess at least about 50% identity (homology) to a native or reference sequence, and preferably, they will be at least about 80%, more preferably at least about 90% identical (homologous) to a native or reference sequence.
• variant mimics are provided.
• the term “variant mimic” is one which contains one or more amino acids which would mimic an activated sequence.
• glutamate may serve as a mimic for phosphoro- threonine and/or phosphoro-serine.
• variant mimics may result in deactivation or in an inactivated product containing the mimic, e.g., phenylalanine may act as an inactivating substitution for tyrosine; or alanine may act as an inactivating substitution for serine.
• homology as it applies to amino acid sequences is defined as the percentage of residues in the candidate amino acid sequence that are identical with the residues in the amino acid sequence of a second sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent homology. Methods and computer programs for the alignment are well known in the art. It is understood that homology depends on a calculation of percent identity but may differ in value due to gaps and penalties introduced in the calculation.
• homologs as it applies to polypeptide sequences means the corresponding sequence of other species having substantial identity to a second sequence of a second species.
• Analogs is meant to include polypeptide variants which differ by one or more amino acid alterations, e.g., substitutions, additions or deletions of amino acid residues that still maintain one or more of the properties of the parent or starting polypeptide.
• compositions which are polypeptide based including variants and derivatives. These include substitutional, insertional, deletion and covalent variants and derivatives.
• derivative is used synonymously with the term “variant” but generally refers to a molecule that has been modified and/or changed in any way relative to a reference molecule or starting molecule.
• sequence tags or amino acids such as one or more lysines
• Sequence tags can be used for peptide purification or localization.
• Lysines can be used to increase peptide solubility or to allow for biotinylation.
• amino acid residues located at the carboxy and amino terminal regions of the amino acid sequence of a peptide or protein may optionally be deleted providing for truncated sequences.
• Certain amino acids e.g., C-terminal or N-terminal residues
• substitutional variants when referring to polypeptides are those that have at least one amino acid residue in a native or starting sequence removed and a different amino acid inserted in its place at the same position.
• the substitutions may be single, where only one amino acid in the molecule has been substituted, or they may be multiple, where two or more amino acids have been substituted in the same molecule.
• conservative amino acid substitution refers to the substitution of an amino acid that is normally present in the sequence with a different amino acid of similar size, charge, or polarity.
• conservative substitutions include the substitution of a non-polar (hydrophobic) residue such as isoleucine, valine and leucine for another non-polar residue.
• conservative substitutions include the substitution of one polar (hydrophilic) residue for another such as between arginine and lysine, between glutamine and asparagine, and between glycine and serine.
• substitution of a basic residue such as lysine, arginine or histidine for another, or the substitution of one acidic residue such as aspartic acid or glutamic acid for another acidic residue are additional examples of conservative substitutions.
• non-conservative substitutions include the substitution of a non-polar (hydrophobic) amino acid residue such as isoleucine, valine, leucine, alanine, methionine for a polar (hydrophilic) residue such as cysteine, glutamine, glutamic acid or lysine and/or a polar residue for a non-polar residue.
• “Insertional variants” when referring to polypeptides are those with one or more amino acids inserted immediately adjacent to an amino acid at a particular position in a native or starting sequence. "Immediately adjacent" to an amino acid means connected to either the alpha-carboxy or alpha-amino functional group of the amino acid.
• deletional variants when referring to polypeptides are those with one or more amino acids in the native or starting amino acid sequence removed. Ordinarily, deletional variants will have one or more amino acids deleted in a particular region of the molecule.
• Covalent derivatives when referring to polypeptides include modifications of a native or starting protein with an organic proteinaceous or non-proteinaceous derivatizing agent, and/or post-translational modifications. Covalent modifications are traditionally introduced by reacting targeted amino acid residues of the protein with an organic derivatizing agent that is capable of reacting with selected side-chains or terminal residues, or by harnessing mechanisms of post-translational modifications that function in selected recombinant host cells. The resultant covalent derivatives are useful in programs directed at identifying residues important for biological activity, for immunoassays, or for the preparation of anti-protein antibodies for immunoaffinity purification of the recombinant glycoprotein. Such modifications are within the ordinary skill in the art and are performed without undue experimentation.
• Certain post-translational modifications are the result of the action of recombinant host cells on the expressed oncology-related polypeptide.
• Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and aspartyl residues. Alternatively, these residues are deamidated under mildly acidic conditions. Either form of these residues may be present in the oncology-related polypeptides produced in accordance with the present invention.
• polypeptides when referring to polypeptides are defined as distinct amino acid sequence-based components of a molecule.
• Features of the polypeptides encoded by the mmRNA of the present invention include surface manifestations, local conformational shape, folds, loops, half-loops, domains, half-domains, sites, termini or any combination thereof.
• surface manifestation refers to a polypeptide based component of a protein appearing on an outermost surface.
• local conformational shape means a polypeptide based structural manifestation of a protein which is located within a definable space of the protein.
• fold refers to the resultant conformation of an amino acid sequence upon energy minimization.
• a fold may occur at the secondary or tertiary level of the folding process.
• secondary level folds include beta sheets and alpha helices.
• tertiary folds include domains and regions formed due to aggregation or separation of energetic forces.
• Regions formed in this way include hydrophobic and hydrophilic pockets, and the like.
• the term "turn” as it relates to protein conformation means a bend which alters the direction of the backbone of a peptide or polypeptide and may involve one, two, three or more amino acid residues.
• loop refers to a structural feature of a polypeptide which may serve to reverse the direction of the backbone of a peptide or polypeptide. Where the loop is found in a polypeptide and only alters the direction of the backbone, it may comprise four or more amino acid residues. Oliva et al. have identified at least 5 classes of protein loops (J. Mol Biol 266 (4): 814- 830; 1997). Loops may be open or closed. Closed loops or "cyclic" loops may comprise 2, 3, 4, 5, 6, 7, 8, 9, 10 or more amino acids between the bridging moieties.
• Such bridging moieties may comprise a cysteine-cysteine bridge (Cys-Cys) typical in polypeptides having disulfide bridges or alternatively bridging moieties may be non-protein based such as the dibromozylyl agents used herein.
• Cys-Cys cysteine-cysteine bridge
• bridging moieties may be non-protein based such as the dibromozylyl agents used herein.
• domain refers to a motif of a polypeptide having one or more identifiable structural or functional characteristics or properties (e.g., binding capacity, serving as a site for protein-protein interactions).
• sub- domains may be identified within domains or half-domains, these subdomains possessing less than all of the structural or functional properties identified in the domains or half domains from which they were derived. It is also understood that the amino acids that comprise any of the domain types herein need not be contiguous along the backbone of the polypeptide (i.e., nonadjacent amino acids may fold structurally to produce a domain, half-domain or subdomain).
• site as it pertains to amino acid based embodiments is used synonymously with "amino acid residue” and "amino acid side chain.”
• a site represents a position within a peptide or polypeptide that may be modified, manipulated, altered, derivatized or varied within the polypeptide based molecules of the present invention.
• terminal refers to an extremity of a peptide or polypeptide. Such extremity is not limited only to the first or final site of the peptide or polypeptide but may include additional amino acids in the terminal regions.
• the polypeptide based molecules of the present invention may be characterized as having both an N-terminus (terminated by an amino acid with a free amino group (NH2)) and a C-terminus (terminated by an amino acid with a free carboxyl group (COOH)).
• Proteins of the invention are in some cases made up of multiple polypeptide chains brought together by disulfide bonds or by non-covalent forces (multimers, oligomers). These sorts of proteins will have multiple N- and C-termini.
• the termini of the polypeptides may be modified such that they begin or end, as the case may be, with a non-polypeptide based moiety such as an organic conjugate.
• any of the features have been identified or defined as a desired component of a polypeptide to be encoded by the signal-sensor primary construct or mmR A of the invention, any of several manipulations and/or modifications of these features may be performed by moving, swapping, inverting, deleting, randomizing or duplicating.
• manipulation of features may result in the same outcome as a modification to the molecules of the invention.
• a manipulation which involved deleting a domain would result in the alteration of the length of a molecule just as modification of a nucleic acid to encode less than a full length molecule would.
• Modifications and manipulations can be accomplished by methods known in the art such as, but not limited to, site directed mutagenesis.
• 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.
• the oncology-related polypeptides may comprise a consensus sequence which is discovered through rounds of experimentation.
• a "consensus" sequence is a single sequence which represents a collective population of sequences allowing for variability at one or more sites.
• protein fragments, functional protein domains, and homologous proteins are also considered to be within the scope of oncology-related polypeptides of interest of this invention.
• any protein fragment meaning an oncology-related polypeptide sequence at least one amino acid residue shorter than a reference oncology-related polypeptide sequence but otherwise identical
• a reference oncology-related protein 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or greater than 100 amino acids in length.
• any oncology- related protein that includes a stretch of about 20, about 30, about 40, about 50, or about 100 amino acids which are about 40%, about 50%, about 60%>, about 70%>, about 80%>, about 90%), about 95%, or about 100% identical to any of the sequences described herein can be utilized in accordance with the invention.
• a polypeptide to be utilized in accordance with the invention includes 2, 3, 4, 5, 6, 7, 8, 9, 10, or more mutations as shown in any of the sequences provided or referenced herein.
• the signal-sensor primary constructs or mmRNA of the present invention may be designed to encode oncology-related polypeptides of interest such as oncology-related peptides and proteins.
• signal-sensor primary constructs or mmRNA of the present invention may encode variant polypeptides which have a certain identity with a reference oncology-related polypeptide sequence.
• a "reference oncology-related polypeptide sequence" refers to a starting oncology-related polypeptide sequence.
• Reference sequences may be wild type sequences or any sequence to which reference is made in the design of another sequence.
• a "reference polypeptide sequence” may, e.g., be any one of the protein sequence listed in Table 6.
• identity refers to a relationship between the sequences of two or more peptides, as determined by comparing the sequences. In the art, identity also means the degree of sequence relatedness between peptides, as determined by the number of matches between strings of two or more amino acid residues. Identity measures the percent of identical matches between the smaller of two or more sequences with gap alignments (if any) addressed by a particular mathematical model or computer program (i.e., "algorithms"). Identity of related peptides can be readily calculated by known methods. Such methods include, but are not limited to, those described in
• the polypeptide variant may have the same or a similar activity as the reference oncology-related polypeptide.
• the variant may have an altered activity (e.g., increased or decreased) relative to a reference oncology- related polypeptide.
• variants of a particular signal-sensor polynucleotide or oncology-related 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%o, 99%) but less than 100% sequence identity to that particular reference signal-sensor polynucleotide or oncology-related 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 F. Altschul, Thomas L. Madden, Alejandro A.
• Default parameters in the BLAST algorithm include, for example, an expect threshold of 10, Word size of 28, Match/Mismatch Scores 1, -2, Gap costs Linear. Any filter can be applied as well as a selection for species specific repeats, e.g., Homo sapiens.
• the signal-sensor polynucleotides, primary constructs and/or mmRNA may be used to treat a disease, disorder and/or condition in a subject.
• the polynucleotides, primary constructs and/or mmRNA may be used to reduce, eliminate or prevent tumor growth in a subject.
• the signal-sensor polynucleotides, primary constructs and/or mmRNA may be used to recude and/or ameliorate at least one symptom of cancer in a subject.
• a symptom of cancer may include, but is not limited to, weakness, aches and pains, fever, fatigue, weight loss, blood clots, increased blood calcium levels, low white blood cell count, short of breath, dizziness, headaches, hyperpigmentation, jaundice, erthema, pruritis, excessive hair growth, change in bowel habits, change in bladder function, long-lasting sores, white patches inside the mouth, white spots on the tongue, unusual bleeding or discharge, thickening or lump on parts of the body, indigestion, trouble swallowing, changes in warts or moles, change in new skin and nagging cough or hoarseness.
• the signal-sensor polynucleotides, primary constructs and/or mmRNA may reduce a side-effect associated with cancer such as, but not limited to, chemo brain, peripheral neuropathy, fatigue, depression, nausea, vomiting, pain, anemia, lymphedema, infections, sexual side effects, reduced fertility or infertility, ostomies, insomnia and hair loss.
• a side-effect associated with cancer such as, but not limited to, chemo brain, peripheral neuropathy, fatigue, depression, nausea, vomiting, pain, anemia, lymphedema, infections, sexual side effects, reduced fertility or infertility, ostomies, insomnia and hair loss.
• the signal-sensor primary constructs or mmRNA disclosed herein may encode one or more validated or "in testing" oncology-related proteins or oncology-related peptides.
• one or more oncology-related proteins or oncology-related peptides currently being marketed or in development may be encoded by the oncology-related signal-sensor polynucleotide, primary constructs or mmRNA of the present invention. While not wishing to be bound by theory, it is believed that incorporation into the signal-sensor primary constructs or mmRNA of the invention will result in improved therapeutic efficacy due at least in part to the specificity, purity and selectivity of the construct designs.
• the signal-sensor polynucleotides, primary constructs and/or mmRNA may alter a biological and/or physiolocial process and/or compound such as, but not limited to, the cell cycle, the DNA damage response (e.g., DNA damage repair), apoptosis, angiogenesis, cell motility, the epithelial to mesenchymal transition in epithelial cells, the phosphatidyl inositol 3 (PI3) kinase/ Akt cellular signaling pathway, telomerase activity and/or expression, tumor metastasis, tumorigenesis, cathepsins, cell senescence, receptor tyrosine kinase signaling, metabolism and drug metabolism, G protein signaling, growth factors and receptors, heat shock proteins, histone deacetylases, hormone receptors, hypoxia, poly ADP-ribose polymerases, protein kinases, RAS signaling, topisomerases, transcription factors and tumor suppressor activity in
• the polynucleotides, primary constructs or mmRNA of the invention may be used to treat cancer which has been caused by carcinogens of natural and/or synthetic origin.
• the use of the polynucleotides, primary constructs and/or mmRNA may be used to treat cancer caused by other organisms and/or cancers caused by viral infection.
• UTRs Untranslated Regions
• Untranslated regions (UTRs) of a gene are transcribed but not translated.
• the 5'UTR starts at the transcription start site and continues to the start codon but does not include the start codon; whereas, the 3'UTR starts immediately following the stop codon and continues until the transcriptional termination signal.
• the regulatory features of a UTR can be incorporated into the signal-sensor polynucleotides, primary constructs and/or mmRNA of the present invention to enhance the stability of the molecule.
• the specific features can also be incorporated to ensure controlled down-regulation of the transcript in case they are misdirected to undesired organs sites.
• the untranslated regions may be incorporated into a vector system which can produce mRNA and/or be delivered to a cell, tissue and/or organism to produce a polypeptide of interest.
• the signal-sensor polynucleotides, primary constructs and/or mmRNA of the present may comprise at least one terminal modification.
• terminal modifications are described in US Provisional Patent Application No US 61/729,933, filed November 26, 2012, entitled Terminally Optimized Modified RNAs, US Provisional Patent application No US 61/737,224, filed December 14, 2012, entitled Terminally Optimized RNAs, US Provisional Patent Application No US 61/758,921, filed January 31, 2013, entitled Differential Targeting Using RNA Constructs, US Provisional Patent Application No. US 61/781,139, filed March 14, 2013, entitled Differential Targeting Using RNA Constructs, US Provisional Patent
• RNA Constructs and US Provisional Patent Application No. 61/857,436, filed July 23, 2013, entitled Differential Targeting Using RNA Constructs, the contents of each of which are herein incorporated by reference in their entireties.
• terminal modifications include, but are not limited to, 5 'caps, microRNA binding sites in the terminal region, chain terminating nucleosides, translation enhancer elements in the terminal region and tailing sequences including a polyA-G quartet and stem loop sequences.
• Natural 5'UTRs bear features which play roles in for translation initiation. They harbor signatures like Kozak sequences which are commonly known to be involved in the process by which the ribosome initiates translation of many genes. Kozak sequences have the consensus CCR(A/G)CCAUGG, where R is a purine (adenine or guanine) three bases upstream of the start codon (AUG), which is followed by another 'G'. 5'UTR also have been known to form secondary structures which are involved in elongation factor binding. For example, one of the secondary 5'-UTR structures is the structured IRES for eIF4A2 elongation factor binding, which is necessary for the microRNA mediated gene repression at 3' -UTR.
• 5'UTR secondary structures involved in elongation factor binding can interact with other RNA binding molecules in the 5'UTR or 3 'UTR to regulate gene expression.
• the elongation factor EIF4A2 binding to a secondarily structured element in the 5'UTR is necessary for microRNA mediated repression (Meijer HA et al., Science, 2013, 340, 82-85, herein incorporated by reference in its entirety).
• the different secondary structures in the 5'UTR can be incorporated into the flanking region to either stabilize or selectively destalized mRNAs in specific tissues or cells.
• mRNA such as albumin, serum amyloid A, Apolipoprotein A/B/E, transferrin, alpha fetoprotein, erythropoietin, or Factor VIII
• tissue-specific mRNA to improve expression in that tissue is possible - for muscle (MyoD, Myosin, Myoglobin, Myogenin, Herculin), for endothelial cells (Tie-1, CD36), for myeloid cells (C/EBP, AML1, G-CSF, GM-CSF, CD1 lb, MSR, Fr-1, i-NOS), for leukocytes (CD45, CD18), for adipose tissue (CD36, GLUT4, ACRP30, adiponectin) and for lung epithelial cells (SP-A/B/C/D).
• non-UTR sequences may be incorporated into the 5' (or 3' UTR) UTRs.
• introns or portions of introns sequences may be incorporated into the flanking regions of the signal-sensor polynucleotides, primary constructs or mmRNA of the invention. Incorporation of intronic sequences may increase protein production as well as mRNA levels.
• TAEs Translation Enhancer Elements
• the 5 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA may include at least one translational enhancer polynucleotide, translation enhancer element, translational enhancer elements (collectively referred to as "TEE"s).
• TEE translational enhancer elements
• the TEE may be located between the transcription promoter and the start codon.
• polynucleotides, primary constructs, modified nucleic acids and/or mmRNA with at least one TEE in the 5 'UTR may include a cap at the 5 'UTR. Further, at least one TEE may be located in the 5 'UTR of signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA undergoing cap-dependent or cap-independent translation.
• translational enhancer element or “translation enhancer element” (herein collectively referred to as “TEE”) refers to sequences that increase the amount of polypeptide or protein produced from an mRNA.
• TEEs are conserved elements in the UTR which can promote translational activity of a nucleic acid such as, but not limited to, cap-dependent or cap-independent translation. The conservation of these sequences has been previously shown by Panek et al (Nucleic Acids Research, 2013, 1-10; herein incorporated by reference in its entirety) across 14 species including humans.
• the TEE may be any of the TEEs listed in Table 35 in Example 45, including portion and/or fragments thereof.
• the TEE sequence may include at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more than 99% of the TEE sequences disclosed in Table 35 and/or the TEE sequence may include a 5-30 nucleotide fragment, a 5-25 nucleotide fragment, a 5-20 nucleotide fragment, a 5-15 nucleotide fragment, a 5-10 nucleotide fragment of the TEE sequences disclosed in Table 35.
• the TEEs known may be in the 5 '-leader of the Gtx homeodomain protein (Chappell et al, Proc. Natl. Acad. Sci. USA 101 :9590-9594, 2004, herein incorporated by reference in their entirety).
• TEEs are disclosed as SEQ ID NOs: 1-35 in US Patent Publication No. US20090226470, SEQ ID NOs: 1-35 in US Patent Publication US20130177581, SEQ ID NOs: 1-35 in International Patent Publication No.
• the TEE may be an internal ribosome entry site (IRES), HCV-IRES or an IRES element such as, but not limited to, those described in US Patent No. US7468275, US Patent Publication Nos. US20070048776 and
• the IRES elements may include, but are not limited to, the Gtx sequences (e.g., Gtx9-nt, Gtx8-nt, Gtx7-nt) described by Chappell et al. (Proc. Natl. Acad. Sci. USA 101 :9590- 9594, 2004) and Zhou et al. (PNAS 102:6273-6278, 2005) and in US Patent Publication Nos. US20070048776 and US20110124100 and International Patent Publication No. WO2007025008, each of which is herein incorporated by reference in its entirety.
• Gtx sequences e.g., Gtx9-nt, Gtx8-nt, Gtx7-nt
• Chappell et al. Proc. Natl. Acad. Sci. USA 101 :9590- 9594, 2004
• Zhou et al. PNAS 102:6273-6278, 2005
• polynucleotide sequences are polynucleotides which include one or more of the specific TEE exemplified herein and/or disclosed in the art (see e.g., US6310197, US6849405, US7456273, US7183395, US20090226470, US20070048776, US20110124100,
• TEEs in the translational enhancer polynucleotides can be organized in one or more sequence segments.
• a sequence segment can harbor one or more of the specific TEEs exemplified herein, with each TEE being present in one or more copies.
• multiple sequence segments When multiple sequence segments are present in a translational enhancer polynucleotide, they can be homogenous or heterogeneous. Thus, the multiple sequence segments in a translational enhancer polynucleotide can harbor identical or different types of the specific TEEs exemplified herein, identical or different number of copies of each of the specific TEEs, and/or identical or different organization of the TEEs within each sequence segment.
• the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA may include at least one TEE that is described in International Patent Publication No. WO1999024595, WO2012009644, WO2009075886, WO2007025008, WO1999024595, European Patent Publication No. EP2610341A1 and EP2610340A1, US Patent No. US6310197, US6849405, US7456273, US7183395, US Patent Publication No. US20090226470, US20110124100, US20070048776,
• the TEE may be located in the 5 'UTR of the signal-sensor
• polynucleotides polynucleotides, primary constructs, modified nucleic acids and/or mmRNA.
• the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA may include at least one TEE that has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 99% identity with the TEEs described in US Patent Publication Nos. US20090226470, US20070048776, US20130177581 and US20110124100, International Patent Publication No. WO1999024595, WO2012009644, WO2009075886 and WO2007025008, European Patent Publication No. EP2610341A1 and EP2610340A1, US Patent No. US6310197, US6849405, US7456273, US7183395, each of which is herein incorporated by reference in its entirety.
• the 5 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA may include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55 or more than 60 TEE sequences.
• the TEE sequences in the 5'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may be the same or different TEE sequences.
• the TEE 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 these patterns, each letter, A, B, or C represent a different TEE sequence at the nucleotide level.
• the 5'UTR may include a spacer to separate two TEE sequences.
• the spacer may be a 15 nucleotide spacer and/or other spacers known in the art.
• the 5'UTR may include a TEE sequence-spacer module repeated at least once, at least twice, at least 3 times, at least 4 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times and at least 9 times or more than 9 times in the 5'UTR.
• the spacer separating two TEE sequences may include other sequences known in the art which may regulate the translation of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention such as, but not limited to, miR sequences described herein (e.g., miR binding sites and miR seeds).
• miR sequences described herein e.g., miR binding sites and miR seeds.
• each spacer used to separate two TEE sequences may include a different miR sequence or component of a miR sequence (e.g., miR seed sequence).
• the TEE in the 5 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may include at least 5%, at least 10%, at least 15%>, at least 20%>, at least 25%>, at least 30%>, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99% or more than 99% of the TEE sequences disclosed in US Patent Publication Nos. US20090226470, US20070048776, US20130177581 and US20110124100,
• the TEE in the 5'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may include a 5-30 nucleotide fragment, a 5-25 nucleotide fragment, a 5-20 nucleotide fragment, a 5-15 nucleotide fragment, a 5-10 nucleotide fragment of the TEE sequences disclosed in US Patent Publication Nos. US20090226470, US20070048776, US20130177581 and US20110124100, International Patent Publication No.
• the TEE in the 5 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may include at least 5%, at least 10%>, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 99%) or more than 99% of the TEE sequences disclosed in Chappell et al. (Proc. Natl. Acad. Sci.
• the TEE in the 5'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may include a 5-30 nucleotide fragment, a 5-25 nucleotide fragment, a 5-20 nucleotide fragment, a 5-15 nucleotide fragment, a 5-10 nucleotide fragment of the TEE sequences disclosed in Chappell et al. (Proc. Natl. Acad. Sci. USA 101 :9590-9594, 2004) and Zhou et al.
• the TEE used in the 5'UTR of the signal-sensor is the TEE used in the 5'UTR of the signal-sensor
• polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention is an IRES sequence such as, but not limited to, those described in US Patent No. US7468275 and International Patent Publication No. WO2001055369, each of which is herein incorporated by reference in its entirety.
• the TEEs used in the 5 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may be identified by the methods described in US Patent Publication No. US20070048776 and US20110124100 and International Patent Publication Nos. WO2007025008 and WO2012009644, each of which is herein incorporated by reference in its entirety.
• the TEEs used in the 5'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may be a transcription regulatory element described in US Patent No. US7456273 and US7183395, US Patent Publication No. US20090093049, and
• WO2001055371 each of which is herein incorporated by reference in their entirety.
• the transcription regulatory elements may be identified by methods known in the art, such as, but not limited to, the methods described in US Patent No. US7456273 and US7183395, US Patent Publication No. US20090093049, and International Publication No. WO2001055371, each of which is herein incorporated by reference in their entirety.
• the TEE used in the 5 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention is an oligonucleotide or portion thereof as described in US Patent No. US7456273 and US7183395, US Patent Publication No. US20090093049, and International Publication No. WO2001055371, each of which is herein incorporated by reference in their entirety.
• the 5' UTR comprising at least one TEE described herein may be incorporated in a monocistronic sequence such as, but not limited to, a vector system or a nucleic acid vector.
• a monocistronic sequence such as, but not limited to, a vector system or a nucleic acid vector.
• the vector systems and nucleic acid vectors may include those described in US Patent Nos. 7456273 and US7183395, US Patent
• the TEEs described herein may be located in the 5 'UTR and/or the 3'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA.
• the TEEs located in the 3'UTR may be the same and/or different than the TEEs located in and/or described for incorporation in the 5 'UTR.
• the 3 'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA may include at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18 at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55 or more than 60 TEE sequences.
• the TEE sequences in the 3'UTR of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention may be the same or different TEE sequences.
• the TEE 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 these patterns, each letter, A, B, or C represent a different TEE sequence at the nucleotide level.
• the 3'UTR may include a spacer to separate two TEE sequences.
• the spacer may be a 15 nucleotide spacer and/or other spacers known in the art.
• the 3'UTR may include a TEE sequence-spacer module repeated at least once, at least twice, at least 3 times, at least 4 times, at least 5 times, at least 6 times, at least 7 times, at least 8 times and at least 9 times or more than 9 times in the 3'UTR.
• the spacer separating two TEE sequences may include other sequences known in the art which may regulate the translation of the signal-sensor polynucleotides, primary constructs, modified nucleic acids and/or mmRNA of the present invention such as, but not limited to, miR sequences described herein (e.g., miR binding sites and miR seeds).
• miR sequences described herein e.g., miR binding sites and miR seeds.
• each spacer used to separate two TEE sequences may include a different miR sequence or component of a miR sequence (e.g., miR seed sequence).
• the incorporation of a miR sequence and/or a TEE sequence changes the shape of the stem loop region which may increase and/or descrease translation, (see e.g, Kedde et al. A Pumilio -induced RNA structure switch in p27-3'UTR controls miR-221 and miR-22 accessibility. Nature Cell Biology. 2010, herein incorporated by reference in its entirety).
• the 5'UTR may comprise at least one microRNA sequence.
• the microRNA sequence may be, but is not limited to, a 19 or 22 nucleotide sequence and/or a microRNA sequence without the seed.
• microRNA sequence in the 5 'UTR may be used to stabilize the nucleic acid and/or mRNA described herein.
• a microRNA sequence in the 5 'UTR may be used to decrease the accessibility of the site of translation initiation such as, but not limited to a start codon.
• Matsuda et al (PLoS One. 2010 1 l(5):e 15057; herein incorporated by reference in its entirety) used antisense locked nucleic acid (LNA) oligonucleotides and exon-junctino complexes (EJCs) around a start codon (-4 to +37 where the A of the AUG codons is +1) in order to decrease the accessibility to the first start codon (AUG).
• LNA antisense locked nucleic acid
• EJCs exon-junctino complexes
• the signal-sensor polynucleotides of the present invention may comprise a microRNA sequence, instead of the LNA or EJC sequence described by Matsuda et al, near the site of translation initiation in order to decrease the accessibility to the site of translation initiation.
• the site of translation initiation may be prior to, after or within the microRNA sequence.
• the site of translation initiation may be located within a microRNA sequence such as a seed sequence or binding site.
• the site of translation initiation may be located within a miR-122 sequence such as the seed sequence or the mir-122 binding site.
• the nucleic acids or mRNA of the present invention comprises at least one microRNA sequence in a region of the nucleic acid or mRNA which may interact with a RNA binding protein.
• RNA Motifs for RNA Binding Proteins (RBPs)
• RNA binding proteins can regulate numerous aspects of co- and post- transcription gene expression such as, but not limited to, RNA splicing, localization, translation, turnover, polyadenylation, capping, modification, export and localization.
• RNA-binding domains such as, but not limited to, RNA recognition motif (RR) and hnRNP K-homology (KH) domains, typically regulate the sequence association between RBPs and their RNA targets (Ray et al. Nature 2013. 499: 172-177; herein incorporated by reference in its entirety).
• the canonical RBDs can bind short RNA sequences.
• the canonical RBDs can recognize structure RNAs.
• the nucleic acids and/or mRNA may comprise at least one RNA-binding motif such as, but not limited to a RNA-binding domain (RBD).
• RBD RNA-binding domain
• the RBD may be any of the RBDs, fragments or variants thereof descried by Ray et al. (Nature 2013. 499: 172-177; herein incorporated by reference in its entirety).
• the nucleic acids or mRNA of the present invention may comprise a sequence for at least one RNA-binding domain (RBDs).
• RBDs RNA-binding domains
• At least one flanking region may comprise at least one RBD.
• the first flanking region and the second flanking region may both comprise at least one RBD.
• the RBD may be the same or each of the RBDs may have at least 60% sequence identity to the other RBD.
• at least on RBD may be located before, after and/or within the 3 'UTR of the nucleic acid or mRNA of the present invention.
• at least one RBD may be located before or within the first 300 nucleosides of the 3'UTR.
• the nucleic acids and/or mRNA of the present invention may comprise at least one RBD in the first region of linked nucleosides.
• the RBD may be located before, after or within a coding region (e.g., the ORF).
• the first region of linked nucleosides and/or at least one flanking region may comprise at least on RBD.
• the first region of linked nucleosides may comprise a RBD related to splicing factors and at least one flanking region may comprise a RBD for stability and/or translation factors.
• the nucleic acids and/or mRNA of the present invention may comprise at least one RBD located in a coding and/or non-coding region of the nucleic acids and/or mRNA.
• At least one RBD may be incorporated into at least one flanking region to increase the stability of the nucleic acid and/or mRNA of the present invention.
• a microRNA sequence in a RNA binding protein motif may be used to decrease the accessibility of the site of translation initiation such as, but not limited to a start codon.
• the signal-sensor polynucleotdies of the present invention may comprise a microRNA sequence, instead of the LNA or EJC sequence described by Matsuda et al, near the site of translation initiation in order to decrease the accessibility to the site of translation initiation.
• the site of translation initiation may be prior to, after or within the microRNA sequence.
• the site of translation initiation may be located within a microRNA sequence such as a seed sequence or binding site.
• the site of translation initiation may be located within a miR-122 sequence such as the seed sequence or the mir-122 binding site.
• an antisense locked nucleic acid LNA
• oligonucleotides and exon-junctino complexes may be used in the RNA binding protein motif.
• the LNA and EJCs may be used around a start codon (-4 to +37 where the A of the AUG codons is +1) in order to decrease the accessibility to the first start codon (AUG).
• 3' UTR and the AU Rich Elements are known to have stretches of Adenosines and Uridines embedded in them. These AU rich signatures are particularly prevalent in genes with high rates of turnover. Based on their sequence features and functional properties, the AU rich elements (AREs) can be separated into three classes (Chen et al, 1995): Class I AREs contain several dispersed copies of an AUUUA motif within U-rich regions. C-Myc and MyoD contain class I AREs. Class II AREs possess two or more overlapping
• AREs containing this type of AREs include GM-CSF and TNF-a. Class III ARES are less well defined. These U rich regions do not contain an AUUUA motif. c-Jun and Myogenin are two well-studied examples of this class. Most proteins binding to the AREs are known to destabilize the messenger, whereas members of the ELAV family, most notably HuR, have been documented to increase the stability of mRNA. HuR binds to AREs of all the three classes. Engineering the HuR specific binding sites into the 3' UTR of nucleic acid molecules will lead to HuR binding and thus, stabilization of the message in vivo.
• AREs 3' UTR AU rich elements
• AREs 3' UTR AU rich elements
• AREs 3' UTR AU rich elements
• AREs can be used to modulate the stability of signal-sensor polynucleotides, primary constructs or mmRNA of the invention.
• one or more copies of an ARE can be introduced to make polynucleotides, primary constructs or mmRNA of the invention less stable and thereby curtail translation and decrease production of the resultant protein.
• AREs can be identified and removed or mutated to increase the intracellular stability and thus increase translation and production of the resultant protein.
• Transfection experiments can be conducted in relevant cell lines, using signal-sensor polynucleotides, primary constructs or mmRNA of the invention and protein production can be assayed at various time points post-transfection.
• cells can be transfected with different ARE- engineering molecules and by using an ELISA kit to the relevant protein and assaying protein produced at 6 hr, 12 hr, 24 hr, 48 hr, and 7 days post-transfection.
• signal-sequence polynucleotides of the present invention may include a triple helix on the 3' end of the signal-sequence polynucleotides.
• the 3' end of the nucleic acids of the present invention may include a triple helix alone or in combination with a Poly-A tail.
• the signal-sequence polynucleotides of the present invention may comprise at least a first and a second U-rich region, a conserved stem loop region between the first and second region and an A-rich region.
• the first and second U- rich region and the A-rich region may associate to form a triple helix on the 3 ' end of the nucleic acid. This triple helix may stabilize the nucleic acid, enhance the translational efficiency of the nucleic acid and/or protect the 3' end from degradation.
• triple helices include, but are not limited to, the triple helix sequence of metastasis- associated lung adenocarcinoma transcript 1 (MALAT1), ⁇ - ⁇ and polyadenylated nuclear (PAN) RNA (See Wilusz et al, Genes & Development 2012 26:2392-2407; herein incorporated by reference in its entirety).
• MALAT1 metastasis- associated lung adenocarcinoma transcript 1
• PAN polyadenylated nuclear
• the 3' end of the modified nucleic acids, enhanced modified RNA or ribonucleic acids of the present invention comprises a first U-rich region comprising TTTTTCTTTT (SEQ ID NO: 1), a second U-rich region comprising TTTTGCTTTTT (SEQ ID NO: 2) or TTTTGCTTTT (SEQ ID NO: 3), an A-rich region comprising AAAAAGCAAAA (SEQ ID NO: 4).
• the 3' end of the nucleic acids of the present invention comprises a triple helix formation structure comprising a first U-rich region, a conserved region, a second U-rich region and an A-rich region.
• the triple helix may be formed from the cleavage of a MALAT1 sequence prior to the cloverleaf structure.
• MALAT1 is a long non-coding RNA which, when cleaved, forms a triple helix and a tRNA-like cloverleaf structure.
• the MALAT1 transcript then localizes to nuclear speckles and the tRNA-like cloverleaf localizes to the cytoplasm (Wilusz et al. Cell 2008 135(5): 919-932; herein incorporated by reference in its entirety).
• the terminal end of the nucleic acid of the present invention comprising the MALAT1 sequence can then form a triple helix structure, after RNaseP cleavage from the cloverleaf structure, which stabilizes the nucleic acid (Peart et al. Non-mRNA 3 ' end formation: how the other half lives; WIREs RNA 2013; herein incorporated by reference in its entirety).
• the signal-sequence polynucleotides described herein comprise a MALAT1 sequence.
• the signal-sequence polynucleotides may be polyadenylated.
• the signal- sequence polynucleotides is not polyadenylated but has an increased resistance to degradation compared to unmodified nucleic acids or mRNA.
• the signal-sequence polynucleotides of the present invention may comprise a MALAT1 sequence in the second flanking region (e.g., the 3'UTR).
• the MALAT1 sequence may be human or mouse.
• the cloverleaf structure of the MALAT1 sequence may also undergo processing by RNaseZ and CCA adding enzyme to form a tRNA-like structure called mascRNA (MALAT1 -associated small cytoplasmic RNA).
• mascRNA MALAT1 -associated small cytoplasmic RNA
• the mascRNA may encode a protein or a fragment thereof and/or may comprise a microRNA sequence.
• the mascRNA may comprise at least one chemical modification described herein.
• the nucleic acids of the present invention may include a stem loop such as, but not limited to, a histone stem loop.
• the stem loop may be a nucleotide sequence that is about 25 or about 26 nucleotides in length such as, but not limited to, SEQ ID NOs: 7-17 as described in International Patent Publication No.
• the histone stem loop may be located 3' relative to the coding region (e.g., at the 3' terminus of the coding region). As a non-limiting example, the stem loop may be located at the 3' end of a nucleic acid described herein.
• the stem loop may be located in the second terminal region.
• the stem loop may be located within an untranslated region (e.g., 3'UTR) in the second terminal region.
• the nucleic acid such as, but not limited to mRNA, which comprises the histone stem loop may be stabilized by the addition of at least one chain terminating nucleoside.
• the addition of at least one chain terminating nucleoside may slow the degradation of a nucleic acid and thus can increase the half-life of the nucleic acid.
• the chain terminating nucleoside may be, but is not limited to, those described in International Patent Publication No. WO2013103659, herein incorporated by reference in its entirety.
• the chain terminating nucleosides which may be used with the present invention includes, but is not limited to, 3'-deoxyadenosine (cordycepin), 3'-deoxyuridine, 3'-deoxycytosine, 3'- deoxyguanosine, 3'-deoxythymine, 2',3'-dideoxynucleosides, such as 2',3'- dideoxyadenosine, 2',3'-dideoxyuridine, 2',3'-dideoxycytosine, 2',3'- dideoxyguanosine, 2',3'-dideoxythymine, a 2'-deoxynucleoside, or a -O- methylnucleoside.
• 3'-deoxyadenosine cordycepin
• 3'-deoxyuridine 3'-deoxycytosine
• 3'- deoxyguanosine 3'-deoxythymine
• the nucleic acid such as, but not limited to mRNA, which comprises the histone stem loop may be stabilized by a modification to the 3 'region of the nucleic acid that can prevent and/or inhibit the addition of oligio(U) (see e.g., International Patent Publication No. WO2013103659, herein incorporated by reference in its entirety).
• the nucleic acid such as, but not limited to mRNA, which comprises the histone stem loop may be stabilized by the addition of an oligonucleotide that terminates in a 3'-deoxynucleoside, 2',3'-dideoxynucleoside 3'-0 ⁇ methy!nucieosides, 3'-0-ethylnucleosides, 3'-arabmosides, and other modified nucleosides known, in the art and/or described herein..
• the nucleic acids of the present invention may include a histone stem loop, a polyA tail sequence and/or a 5 'cap structure.
• the histone stem loop may be before and/or after the polyA tail sequence.
• the nucleic acids comprising the histone stem loop and a polyA tail sequence may include a chain terminating nucleoside described herein.
• the nucleic acids of the present invention may include a histone stem loop and a 5 'cap structure.
• the 5 'cap structure may include, but is not limited to, those described herein and/or known in the art.
• the conserved stem loop region may comprise a miR sequence described herein.
• the stem loop region may comprise the seed sequence of a miR sequence described herein.
• the stem loop region may comprise a miR- 122 seed sequence.
• the conserved stem loop region may comprise a miR sequence described herein and may also include a TEE sequence.
• the incorporation of a miR sequence and/or a TEE sequence changes the shape of the stem loop region which may increase and/or descrease translation, (see e.g, Kedde et al. A Pumilio -induced RNA structure switch in p27-3'UTR controls miR-221 and miR-22 accessibility. Nature Cell Biology. 2010, herein incorporated by reference in its entirety).
• the 5' cap structure of an mRNA is involved in nuclear export, increasing mRNA stability and binds the mRNA Cap Binding Protein (CBP), which is responsibile for mRNA stability in the cell and translation competency through the association of CBP with poly(A) binding protein to form the mature cyclic mRNA species.
• CBP mRNA Cap Binding Protein
• the cap further assists the removal of 5' proximal introns removal during mRNA splicing.
• Endogenous mRNA molecules may be 5 '-end capped generating a 5'-ppp-5'- triphosphate linkage between a terminal guanosine cap residue and the 5 '-terminal transcribed sense nucleotide of the mRNA molecule.
• This 5'-guanylate cap may then be methylated to generate an N7-methyl-guanylate residue.
• the ribose sugars of the terminal and/or anteterminal transcribed nucleotides of the 5' end of the mRNA may optionally also be 2'-0-methylated.
• 5'-decapping through hydrolysis and cleavage of the guanylate cap structure may target a nucleic acid molecule, such as an mRNA molecule, for degradation.
• Modifications to the signal-sensor polynucleotides, primary constructs, and mmRNA of the present invention may generate a non-hydrolyzable cap structure preventing decapping and thus increasing mRNA half-life. Because cap structure hydrolysis requires cleavage of 5'-ppp-5' phosphorodiester linkages, modified nucleotides may be used during the capping reaction. For example, a Vaccinia Capping Enzyme from New England Biolabs (Ipswich, MA) may be used with a-thio-guanosine nucleotides according to the manufacturer's instructions to create a phosphorothioate linkage in the 5'-ppp-5' cap.
• a Vaccinia Capping Enzyme from New England Biolabs (Ipswich, MA) may be used with a-thio-guanosine nucleotides according to the manufacturer's instructions to create a phosphorothioate linkage in the 5'-ppp-5' cap.
• Additional modified guanosine nucleotides may be used such as a-methyl-phosphonate and seleno-phosphate nucleotides.
• Additional modifications include, but are not limited to, 2'-0-methylation of the ribose sugars of 5 '-terminal and/or 5'-anteterminal nucleotides of the mR A (as mentioned above) on the 2'-hydroxyl group of the sugar ring.
• Multiple distinct 5 '-cap structures can be used to generate the 5 '-cap of a nucleic acid molecule, such as an mRNA molecule.
• Cap analogs which herein are also referred to as synthetic cap analogs, chemical caps, chemical cap analogs, or structural or functional cap analogs, differ from natural (i.e. endogenous, wild-type or physiological) 5'-caps in their chemical structure, while retaining cap function. Cap analogs may be chemically (i.e. non-enzymatically) or enzymatically synthesized and/linked to a nucleic acid molecule.
• the Anti-Reverse Cap Analog (ARCA) cap contains two guanines linked by a 5 '-5 '-triphosphate group, wherein one guanine contains an N7 methyl group as well as a 3'-0-methyl group (i.e., N7,3'-0-dimethyl-guanosine-5'-triphosphate-5'- guanosine (m 7 G-3'mppp-G; which may equivaliently be designated 3' O-Me- m7G(5')ppp(5')G).
• the 3'-0 atom of the other, unmodified, guanine becomes linked to the 5 '-terminal nucleotide of the capped nucleic acid molecule (e.g. an mRNA or mmRNA).
• the N7- and 3'-0-methlyated guanine provides the terminal moiety of the capped nucleic acid molecule (e.g. mRNA or mmRNA).
• mCAP which is similar to ARCA but has a 2'-0- methyl group on guanosine (i.e., N7,2'-0-dimethyl-guanosine-5'-triphosphate-5'- guanosine, m 7 Gm-ppp-G).
• cap analogs allow for the concomitant capping of a nucleic acid molecule in an in vitro transcription reaction, up to 20% of transcripts remain uncapped. This, as well as the structural differences of a cap analog from an endogenous 5 '-cap structures of nucleic acids produced by the endogenous, cellular transcription machinery, may lead to reduced translational competency and reduced cellular stability.
• Signal-sensor polynucleotides, primary constructs and mmRNA of the invention may also be capped post-transcriptionally, using enzymes, in order to generate more authentic 5 '-cap structures.
• the phrase "more authentic” refers to a feature that closely mirrors or mimics, either structurally or functionally, an endogenous or wild type feature. That is, a "more authentic" feature is better representative of an endogenous, wild-type, natural or physiological cellular function and/or structure as compared to synthetic features or analogs, etc., of the prior art, or which outperforms the corresponding endogenous, wild-type, natural or physiological feature in one or more respects.
• Non- limiting examples of more authentic 5 'cap structures of the present invention are those which, among other things, have enhanced binding of cap binding proteins, increased half life, reduced susceptibility to 5' endonucleases and/or reduced 5'decapping, as compared to synthetic 5 'cap structures known in the art (or to a wild-type, natural or physiological 5 'cap structure).
• recombinant Vaccinia Virus Capping Enzyme and recombinant 2'-0-methyltransferase enzyme can create a canonical 5 '-5 '-triphosphate linkage between the 5 '-terminal nucleotide of an mRNA and a guanine cap nucleotide wherein the cap guanine contains an N7 methylation and the 5 '-terminal nucleotide of the mRNA contains a 2'-0-methyl.
• Capl structure Such a structure is termed the Capl structure.
• Cap structures include 7mG(5')ppp(5')N,pN2p (cap 0), 7mG(5')ppp(5')NlmpNp (cap 1), and 7mG(5')-ppp(5')NlmpN2mp (cap 2).
• the signal-sensor polynucleotides, primary constructs or mmRNA may be capped post-transcriptionally, and because this process is more efficient, nearly 100% of the signal-sensor polynucleotides, primary constructs or mmRNA may be capped. This is in contrast to -80% when a cap analog is linked to an mRNA in the course of an in vitro transcription reaction.
• 5' terminal caps may include endogenous caps or cap analogs.
• a 5' terminal cap may comprise a guanine analog.
• Useful guanine analogs include inosine, Nl-methyl-guanosine, 2'fluoro-guanosine, 7-deaza-guanosine, 8-oxo-guanosine, 2-amino-guanosine, LNA- guanosine, and 2-azido-guanosine.
• Additional viral sequences such as, but not limited to, the translation enhancer sequence of the barley yellow dwarf virus (BYDV-PAV) can be engineered and inserted in the 3' UTR of the signal-sensor polynucleotides, primary constructs or mmRNA of the invention and can stimulate the translation of the construct in vitro and in vivo.
• Transfection experiments can be conducted in relevant cell lines at and protein production can be assayed by ELISA at 12hr, 24hr, 48hr, 72 hr and day 7 post- transfection.
• signal-sensor polynucleotides, primary constructs or mmRNA which may contain an internal ribosome entry site (IRES).
• IRES internal ribosome entry site
• An IRES may act as the sole ribosome binding site, or may serve as one of multiple ribosome binding sites of an mRNA.
• signal-sensor polynucleotides, primary constructs or mmRNA containing more than one functional ribosome binding site may encode several oncology-related peptides or oncology-related polypeptides that are translated independently by the ribosomes ("multicistronic nucleic acid molecules").
• IRES sequences that can be used according to the invention include without limitation, those from picornaviruses (e.g. FMDV), pest viruses (CFFV), polio viruses (PV), encephalomyocarditis viruses (ECMV), foot-and-mouth disease viruses (FMDV), hepatitis C viruses (HCV), classical swine fever viruses (CSFV), murine leukemia virus (MLV), simian immune deficiency viruses (SIV) or cricket paralysis viruses (CrPV).
• picornaviruses e.g. FMDV
• CFFV pest viruses
• PV polio viruses
• ECMV encephalomyocarditis viruses
• FMDV foot-and-mouth disease viruses
• HCV hepatitis C viruses
• CSFV classical swine fever viruses
• MLV murine leukemia virus
• SIV simian immune deficiency viruses
• CrPV cricket paralysis viruses
• a long chain of adenine nucleotides may be added to a polynucleotide such as an mRNA molecule in order to increase stability.
• a polynucleotide such as an mRNA molecule
• the 3' end of the transcript may be cleaved to free a 3' hydroxyl.
• poly-A polymerase adds a chain of adenine nucleotides to the RNA.
• the process, called polyadenylation adds a poly-A tail that can be between 100 and 250 residues long.
• the length of a poly-A tail of the present invention is greater than 30 nucleotides in length.
• the poly-A tail is greater than 35 nucleotides in length (e.g., at least or greater than about 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, 1,000, 1,100, 1,200, 1,300, 1,400, 1,500, 1,600, 1,700, 1,800, 1,900, 2,000, 2,500, and 3,000 nucleotides).
• the signal-sensor polynucleotides, primary construct, or mmRNA includes from about 30 to about 3,000 nucleotides (e.g., from 30 to 50, from 30 to 100, from 30 to 250, from 30 to 500, from 30 to 750, from 30 to 1,000, from 30 to 1,500, from 30 to 2,000, from 30 to 2,500, from 50 to 100, from 50 to 250, from 50 to 500, from 50 to 750, from 50 to 1,000, from 50 to 1,500, from 50 to 2,000, from 50 to 2,500, from 50 to 3,000, from 100 to 500, from 100 to 750, from 100 to 1,000, from 100 to 1,500, from 100 to 2,000, from 100 to 2,500, from 100 to 3,000, from 500 to 750, from 500 to 1,000, from 500 to 1,500, from 500 to 2,000, from 500 to 2,500, from 500 to 3,000, from 1,000 to 1,500, from 1,000 to 2,000, from 1,000 to 2,500, from 1,000 to 3,000, from 1,500 to 2,000, from 1,500 to 2,500, from 1,500 to
• the poly-A tail is designed relative to the length of the overall signal-sensor polynucleotides, primary constructs or mmRNA. This design may be based on the length of the coding region, the length of a particular feature or region (such as the first or flanking regions), or based on the length of the ultimate product expressed from the polynucleotides, primary constructs or mmRNA.
• the poly-A tail may be 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100% greater in length than the signal-sensor polynucleotides, primary constructs or mmRNA or feature thereof.
• the poly-A tail may also be designed as a fraction of polynucleotides, primary constructs or mmRNA to which it belongs.
• the poly-A tail may be 10, 20, 30, 40, 50, 60, 70, 80, or 90% or more of the total length of the construct or the total length of the construct minus the poly-A tail.
• engineered binding sites and/or conjugation of signal- sensor polynucleotides, primary constructs or mmRNA for Poly-A binding protein may be used to enhance expression.
• the engineered binding sites may be sensor sequences which can operate as binding sites for ligands of the local microenvironment of the nucleic acids and/or mRNA.
• the nucleic acids and/or mRNA may comprise at least one engineered binding site to alter the binding affinity of Poly-A binding protein (PABP) and analogs thereof.
• PABP Poly-A binding protein
• the incorporation of at least one engineered binding site may increase the binding affinity of the PABP and analogs thereof.
• multiple distinct signal-sensor polynucleotides, primary constructs or mmRNA may be linked together to the PABP (Poly- A binding protein) through the 3'- end using modified nucleotides at the 3 '-terminus of the poly-A tail.
• Transfection experiments can be conducted in relevant cell lines and protein production can be assayed by ELISA at 12hr, 24hr, 48hr, 72 hr and day 7 post-transfection.
• the transfection experiments may be used to evaluate the effect on PABP or analogs thereof binding affinity as a result of the addition of at least one engineered binding site.
• the signal-sensor polynucleotides and primary constructs of the present invention are designed to include a polyA-G quartet.
• the G-quartet is a cyclic hydrogen bonded array of four guanine nucleotides that can be formed by G-rich sequences in both DNA and RNA.
• the G-quartet is incorporated at the end of the poly-A tail.
• the resultant mmRNA construct is assayed for stability, protein production and other parameters including half- life at various time points. It has been discovered that the polyA-G quartet results in protein production equivalent to at least 75% of that seen using a poly-A tail of 120 nucleotides alone.
• the nucleic acids or mRNA of the present invention may comprise a polyA tail and may be stabilized by the addition of a chain terminating nucleoside.
• the nucleic acids and/or mRNA with a polyA tail may further comprise a 5 'cap structure.
• the nucleic acids or mRNA of the present invention may comprise a polyA-G quartet.
• the nucleic acids and/or mRNA with a polyA-G quartet may further comprise a 5 'cap structure.
• the chain terminating nucleoside which may be used to stabilize the nucleic acid or mRNA comprising a polyA tail or polyA-G quartet may be, but is not limited to, those described in International Patent Publication No.
• the chain terminating nucleosides which may be used with the present invention includes, but is not limited to, 3'-deoxyadenosine (cordycepin), 3'- deoxyuridine, 3'-deoxycytosine, 3'-deoxyguanosine, 3'-deoxythymine, 2',3'- dideoxynucleosides, such as 2',3'- dideoxyadenosine, 2',3'-dideoxyuridine, 2',3'- dideoxycytosine, 2',3'- dideoxyguanosine, 2',3'-dideoxythymine, a 2'-deoxynucleoside, or a -O- methylnucleoside.
• 3'-deoxyadenosine cordycepin
• 3'- deoxyuridine 3'-deoxycytosine
• 3'-deoxyguanosine 3'-deoxythymine
• the nucleic acid such as, but not limited to mR A, which comprise a polyA tail or a polyA-G quartet may be stabilized by a modification to the 3 'region of the nucleic acid that can prevent and/or inhibit the addition of oligio(U) (see e.g., International Patent Publication No. WO2013103659, herein incorporated by reference in its entirety).
• the nucleic acid such as, but not limited to mRNA, which comprise a polyA tail or a polyA-G quartet may be stabilized by the addition of an oligonucleotide that terminates in a 3'-deoxynucleoside, 2', 3'- dideoxynucleoside 3 -0- methylnucSeosides, 3' ⁇ Q ⁇ eihyimic]eosides, 3'-arabinosides, and other modified nucleosides known in the art and/or described herein.
• the signal-sensor polynucleotides, primary constructs or mmRNA of the present invention may be quantified in exosomes derived from one or more bodily fluid.
• bodily fluids include peripheral blood, serum, plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bone marrow, synovial fluid, aqueous humor, amniotic fluid, cerumen, breast milk, broncheoalveolar lavage fluid, semen, prostatic fluid, cowper's fluid or pre-ejaculatory fluid, sweat, fecal matter, hair, tears, cyst fluid, pleural and peritoneal fluid, pericardial fluid, lymph, chyme, chyle, bile, interstitial fluid, menses, pus, sebum, vomit, vaginal secretions, mucosal secretion, stool water, pancreatic juice, lavage fluids from sinus cavities, bronchopulmonary aspirates, blasto
• exosomes may be retrieved from an organ selected from the group consisting of lung, heart, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colon, breast, prostate, brain, esophagus, liver, and placenta.
• the level or concentration of signal-sensor polynucleotides, primary construct or mmRNA may be an expression level, presence, absence, truncation or alteration of the administered construct. It is advantageous to correlate the level with one or more clinical phenotypes or with an assay for a human disease biomarker.
• the assay may be performed using construct specific probes, cytometry, qRT-PCR, real-time PCR, PCR, flow cytometry, electrophoresis, mass spectrometry, or combinations thereof while the exosomes may be isolated using immunohistochemical methods such as enzyme linked immunosorbent assay (ELISA) methods. Exosomes may also be isolated by size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfiuidic separation, or combinations thereof.
• immunohistochemical methods such as enzyme linked immunosorbent assay (ELISA) methods.
• Exosomes may also be isolated by size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfiuidic separation, or combinations thereof.
• Signal-sensor polynucleotides, primary constructs or mmRNA for use in accordance with the invention may be prepared according to any available technique including, but not limited to chemical synthesis, enzymatic synthesis, which is generally termed in vitro transcription (IVT) or enzymatic or chemical cleavage of a longer precursor, etc.
• IVT in vitro transcription
• Methods of synthesizing RNAs are known in the art (see, e.g., Gait, M.J. (ed.) Oligonucleotide synthesis: a practical approach, Oxford [Oxfordshire],
• the process of design and synthesis of the signal-sensor primary constructs of the invention generally includes the steps of gene construction, mRNA production (either with or without modifications) and purification.
• a target signal-sensor polynucleotide sequence encoding the oncology-related polypeptide of interest is first selected for incorporation into a vector which will be amplified to produce a cDNA template.
• the target signal-sensor polynucleotide sequence and/or any flanking sequences may be codon optimized.
• the cDNA template is then used to produce mRNA through in vitro transcription (IVT). After production, the mRNA may undergo purification and clean-up processes. The steps of which are provided in more detail below.
• the step of gene construction may include, but is not limited to gene synthesis, vector amplification, plasmid purification, plasmid linearization and clean-up, and cDNA template synthesis and clean-up.
• a signal-sensor primary construct is designed.
• a first region of linked nucleosides encoding the polypeptide of interest may be constructed using an open reading frame (ORF) of a selected nucleic acid (DNA or RNA) transcript.
• the ORF may comprise the wild type ORF, an isoform, variant or a fragment thereof.
• an "open reading frame” or “ORF” is meant to refer to a nucleic acid sequence (DNA or RNA) which is capable of encoding an oncology-related polypeptide of interest. ORFs often begin with the start codon, ATG and end with a nonsense or termination codon or signal.
• the nucleotide sequence of the first region may be codon optimized. 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 GC content to increase mRNA 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 trafficking sequences, remove/add post translation modification sites in encoded protein (e.g.
• Codon optimization tools, algorithms and services are known in the art, non- limiting examples include services from GeneArt (Life Technologies) and/or DNA2.0 (Menlo Park CA).
• the ORF sequence is optimized using optimization algorithms. Codon options for each amino acid are given in Table 1.
• nucleotide sequence after a nucleotide sequence has been codon optimized it may be further evaluated for regions containing restriction sites. At least one nucleotide within the restriction site regions may be replaced with another nucleotide in order to remove the restriction site from the sequence but the replacement of nucleotides does alter the amino acid sequence which is encoded by the codon optimized nucleotide sequence.
• flanking regions may be incorporated into the signal-sensor primary construct before and/or after optimization of the ORF. It is not required that a signal-sensor primary construct contain both a 5' and 3' flanking region. Examples of such features include, but are not limited to, untranslated regions (UTRs), Kozak sequences, an oligo(dT) sequence, and detectable tags and may include multiple cloning sites which may have Xbal recognition.
• a 5' UTR and/or a 3' UTR may be provided as flanking regions. Multiple 5 ' or 3' UTRs may be included in the flanking regions and may be the same or of different sequences. Any portion of the flanking regions, including none, may be codon optimized and any may independently contain one or more different structural or chemical modifications, before and/or after codon optimization. Combinations of features may be included in the first and second flanking regions and may be contained within other features.
• the ORF may be flanked by a 5' UTR which may contain a strong Kozak translational initiation signal and/or a 3' UTR which may include an oligo(dT) sequence for templated addition of a poly-A tail.
• Tables 2 and 3 provide a listing of exemplary UTRs which may be utilized in the signal-sensor primary construct of the present invention as flanking regions. Shown in Table 2 is a representative listing of a 5 '-untranslated region of the invention. Variants of 5 ' UTRs may be utilized wherein one or more nucleotides are added or removed to the termini, including A, T, C or G.
• Table 3 Shown in Table 3 is a representative listing of 3 '-untranslated regions of the invention. Variants of 3 ' UTRs may be utilized wherein one or more nucleotides are added or removed to the termini, including A, T, C or G.
• CACATCTACTTGCTTAAATTGTGGGCAAAAGAG collagen AAAAAGAAGGATTGATCAGAGCATTGTGCAATAUTR-007 1 1 type I, alpha CAGTTTCATTAACTCCTTCCCCCGCTCCCCCAAA
• GGGGCTAGAGCCCTCTCCGCACAGCGTGGAGAC GGGGCAAGGAGGGGGGTTATTAGGATTGGTGGT TTTGTTTTGCTTTGTTTAAAGCCGTGGGAAAATG GCACAACTTTACCTCTGTGGGAGATGCAACACT
• LRP1 low TCCTGCCCCCTGCCAGTGAAGTCCTTCAGTGAGC density CCCTCCCCAGCCAGCCCTTCCCTGGCCCCGCCGG lipoprotein ATGTATAAATGTAAAAATGAAGGAATTACATTTUTR-010 14 receptor- TATATGTGAGCGAGCAAGCCGGCAAGCGAGCAC related AGTATTATTTCTCCATCCCCTCCCTGCCTGCTCCT protein 1 TGGCACCCCCATGCTGCCTTCAGGGAGACAGGC
• CCACTTTCACAGCCTCCAAGTCTGTGGCTCTTCCUTR-016 nucleobindi CTTCTGTCCTCCGAGGGGCTTGCCTTCTCTCGTG 20 n 1 TCCAGTGAGGTGCTCAGTGATCGGCTTAACTTAG
• any UTR from any gene may be incorporated into the respective first or second flanking region of the primary construct.
• multiple wild-type UTRs of any known gene may be utilized. It is also within the scope of the present invention to provide artificial UTRs which are not variants of wild type genes. These UTRs or portions thereof may be placed in the same orientation as in the transcript from which they were selected or may be altered in orientation or location. Hence a 5 ' or 3' UTR may be inverted, shortened, lengthened, made chimeric with one or more other 5' UTRs or 3' UTRs.
• the term "altered" as it relates to a UTR sequence means that the UTR has been changed in some way in relation to a reference sequence.
• a 3' or 5' UTR may be altered relative to a wild type or native UTR by the change in orientation or location as taught above or may be altered by the inclusion of additional nucleotides, deletion of nucleotides, swapping or transposition of nucleotides. Any of these changes producing an "altered" UTR (whether 3' or 5') comprise a variant UTR.
• a double, triple or quadruple UTR such as a 5' or 3' UTR may be used.
• a "double" UTR is one in which two copies of the same UTR are encoded either in series or substantially in series.
• a double beta- globin 3' UTR may be used as described in US Patent publication 20100129877, the contents of which are incorporated herein by reference in its entirety.
• patterned UTRs are those UTRs which reflect a repeating or alternating pattern, such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than 3 times.
• each letter, A, B, or C represent a different UTR at the nucleotide level.
• flanking regions are selected from a family of transcripts whose proteins share a common function, structure, feature of property.
• oncology-related polypeptides of interest may belong to a family of proteins which are expressed in a particular cell, tissue or at some time during development.
• the UTRs from any of these genes may be swapped for any other UTR of the same or different family of proteins to create a new chimeric primary transcript.
• a "family of proteins" is used in the broadest sense to refer to a group of two or more oncology-related polypeptides of interest which share at least one function, structure, feature, localization, origin, or expression pattern.
• the signal-sensor primary construct components are reconstituted and transformed into a vector such as, but not limited to, plasmids, viruses, cosmids, and artificial chromosomes.
• a vector such as, but not limited to, plasmids, viruses, cosmids, and artificial chromosomes.
• the optimized construct may be reconstituted and transformed into chemically competent E. coli, yeast, neurospora, maize, drosophila, etc. where high copy plasmid-like or chromosome structures occur by methods described herein.
• the signal-sensor primary constructs of the present invention may include at least two stop codons before the 3' untranslated region (UTR).
• the stop codon may be selected from TGA, TAA and TAG.
• the signal-sensor primary constructs of the present invention include the stop codon TGA and one additional stop codon.
• the addition stop codon may be TAA.
• the vector containing the signal-sensor primary construct is then amplified and the plasmid isolated and purified using methods known in the art such as, but not limited to, a maxi prep using the Invitrogen PURELINKTM HiPure Maxiprep Kit (Carlsbad, CA). Plasmid Linearization
• the plasmid may then be linearized using methods known in the art such as, but not limited to, the use of restriction enzymes and buffers.
• the linearization reaction may be purified using methods including, for example Invitrogen's PURELINKTM PCR Micro Kit (Carlsbad, CA), and HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP- HPLC), and hydrophobic interaction HPLC (HIC-HPLC) and Invitrogen's standard PURELINKTM PCR Kit (Carlsbad, CA).
• the purification method may be modified depending on the size of the linearization reaction which was conducted.
• the linearized plasmid is then used to generate cDNA for in vitro transcription (IVT) reactions.
• IVT in vitro transcription
• a cDNA template may be synthesized by having a linearized plasmid undergo polymerase chain reaction (PCR).
• Table 4 is a listing of primers and probes that may be useful in the PCR reactions of the present invention. It should be understood that the listing is not exhaustive and that primer-probe design for any amplification is within the skill of those in the art. Probes may also contain chemically modified bases to increase base-pairing fidelity to the target molecule and base-pairing strength. Such modifications may include 5-methyl-Cytidine, 2, 6-di-amino-purine, 2'-fluoro, phosphoro-thioate, or locked nucleic acids.
• URP universal forward primer
• URP universal reverse primer
• the cDNA may be submitted for sequencing analysis before undergoing transcription.
• Signal-sensor polynucleotide Production (signal-sensor mRNA)
• the process of signal-sensor polynucleotide production may include, but is not limited to, in vitro transcription, cDNA template removal and RNA clean-up, and capping and/or tailing reactions.
• the cDNA produced in the previous step may be transcribed using an in vitro transcription (IVT) system.
• the system typically comprises a transcription buffer, nucleotide triphosphates (NTPs), an RNase inhibitor and a polymerase.
• NTPs may be manufactured in house, may be selected from a supplier, or may be synthesized as described herein.
• the NTPs may be selected from, but are not limited to, those described herein including natural and unnatural (modified) NTPs.
• the polymerase may be selected from, but is not limited to, T7 RNA polymerase, T3 RNA polymerase and mutant polymerases such as, but not limited to, polymerases able to be incorporated into modified nucleic acids.
• RNA polymerases or variants may be used in the design of the signal-sensor primary constructs of the present invention.
• RNA polymerases may be modified by inserting or deleting amino acids of the RNA polymerase sequence.
• the RNA polymerase may be modified to exhibit an increased ability to incorporate a 2 '-modified nucleotide triphosphate compared to an unmodified RNA polymerase (see International Publication WO2008078180 and U.S. Patent 8,101,385; herein incorporated by reference in their entireties).
• Variants may be obtained by evolving an RNA polymerase, optimizing the RNA polymerase amino acid and/or nucleic acid sequence and/or by using other methods known in the art.
• T7 RNA polymerase variants may be evolved using the continuous directed evolution system set out by Esvelt et al. (Nature (2011) 472(7344):499-503; herein incorporated by reference in its entirety) where clones of T7 RNA polymerase may encode at least one mutation such as, but not limited to, lysine at position 93 substituted for threonine (K93T), I4M, A7T, E63V, V64D, A65E, D66Y, T76N, C125R, S128R, A136T, N165S, G175R, H176L, Y178H, F182L, L196F, G198V, D208Y, E222K, S228A, Q239R, T243N, G259D, M267I, G280C, H300R, D351A, A354S, E356D, L360P, A383V, Y385C, D3
• K93T ly
• T7 RNA polymerase variants may encode at least mutation as described in U.S. Pub. Nos. 20100120024 and 20070117112; herein incorporated by reference in their entireties.
• Variants of RNA polymerase may also include, but are not limited to, substitutional variants, conservative amino acid
• the signal-sensor primary construct may be designed to be recognized by the wild type or variant RNA polymerases. In doing so, the signal-sensor primary construct may be modified to contain sites or regions of sequence changes from the wild type or parent primary construct.
• the signal-sensor primary construct may be designed to include at least one substitution and/or insertion upstream of an RNA polymerase binding or recognition site, downstream of the RNA polymerase binding or recognition site, upstream of the TATA box sequence, downstream of the TATA box sequence of the signal-sensor primary construct but upstream of the coding region of the primary construct, within the 5'UTR, before the 5'UTR and/or after the 5'UTR.
• the 5 'UTR of the signal-sensor primary construct may be replaced by the insertion of at least one region and/or string of nucleotides of the same base.
• the region and/or string of nucleotides may include, but is not limited to, at least 3, at least 4, at least 5, at least 6, at least 7 or at least 8 nucleotides and the nucleotides may be natural and/or unnatural.
• the group of nucleotides may include 5-8 adenine, cytosine, thymine, a string of any of the other nucleotides disclosed herein and/or combinations thereof.
• the 5 'UTR of the signal-sensor primary construct may be replaced by the insertion of at least two regions and/or strings of nucleotides of two different bases such as, but not limited to, adenine, cytosine, thymine, any of the other nucleotides disclosed herein and/or combinations thereof.
• the 5'UTR may be replaced by inserting 5-8 adenine bases followed by the insertion of 5-8 cytosine bases.
• the 5'UTR may be replaced by inserting 5-8 cytosine bases followed by the insertion of 5-8 adenine bases.
• the signal-sensor primary construct may include at least one substitution and/or insertion downstream of the transcription start site which may be recognized by an RNA polymerase.
• at least one substitution and/or insertion may occur downstream the transcription start site by substituting at least one nucleic acid in the region just downstream of the transcription start site (such as, but not limited to, +1 to +6).
• NTP nucleotide triphosphate
• the signal-sensor primary construct may include the substitution of at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12 or at least 13 guanine bases downstream of the transcription start site.
• the signal-sensor primary construct may include the substitution of at least 1, at least 2, at least 3, at least 4, at least 5 or at least 6 guanine bases in the region just downstream of the transcription start site.
• the guanine bases may be substituted by at least 1, at least 2, at least 3 or at least 4 adenine nucleotides.
• the nucleotides in the region are GGGAGA the guanine bases may be substituted by at least 1, at least 2, at least 3 or at least 4 cytosine bases.
• the guanine bases in the region are GGGAGA the guanine bases may be substituted by at least 1, at least 2, at least 3 or at least 4 thymine, and/or any of the nucleotides described herein.
• the signal-sensor primary construct may include at least one substitution and/or insertion upstream of the start codon.
• the start codon is the first codon of the protein coding region whereas the transcription start site is the site where transcription begins.
• the signal-sensor primary construct may include, but is not limited to, at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7 or at least 8 substitutions and/or insertions of nucleotide bases.
• the nucleotide bases may be inserted or substituted at 1, at least 1, at least 2, at least 3, at least 4 or at least 5 locations upstream of the start codon.
• the nucleotides inserted and/or substituted may be the same base (e.g., all A or all C or all T or all G), two different bases (e.g., A and C, A and T, or C and T), three different bases (e.g., A, C and T or A, C and T) or at least four different bases.
• the guanine base upstream of the coding region in the signal-sensor primary construct may be substituted with adenine, cytosine, thymine, or any of the nucleotides described herein.
• the substitution of guanine bases in the signal-sensor primary construct may be designed so as to leave one guanine base in the region downstream of the transcription start site and before the start codon (see Esvelt et al. Nature (2011) 472(7344):499-503; herein incorporated by reference in its entirety).
• at least 5 nucleotides may be inserted at 1 location
• RNA clean-up may also include a purification method such as, but not limited to, AGENCOURT®
• CLEANSEQ® system from Beckman Coulter (Danvers, MA), HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC- HPLC) .
• the signal-sensor primary construct or mmRNA may also undergo capping and/or tailing reactions.
• a capping reaction may be performed by methods known in the art to add a 5' cap to the 5' end of the signal-sensor primary construct. Methods for capping include, but are not limited to, using a Vaccinia Capping enzyme (New England Biolabs, Ipswich, MA).
• a poly-A tailing reaction may be performed by methods known in the art, such as, but not limited to, 2' O-methyltransferase and by methods as described herein. If the signal-sensor primary construct generated from cDNA does not include a poly-T, it may be beneficial to perform the poly-A-tailing reaction before the signal-sensor primary construct is cleaned.
• Signal-sensor primary construct or mmRNA purification may include, but is not limited to, mRNA or mmRNA clean-up, quality assurance and quality control.
• mRNA or mmRNA clean-up may be performed by methods known in the arts such as, but not limited to, AGENCOURT® beads (Beckman Coulter Genomics, Danvers, MA), poly-T beads, LNATM oligo-T capture probes (EXIQON® Inc, Vedbaek, Denmark) or HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC-HPLC).
• AGENCOURT® beads Beckman Coulter Genomics, Danvers, MA
• poly-T beads poly-T beads
• LNATM oligo-T capture probes EXIQON® Inc, Vedbaek, Denmark
• HPLC based purification methods such as, but not limited to, strong anion
• purified when used in relation to a polynucleotide such as a “purified mRNA or signal-sensor mmRNA” refers to one that is separated from at least one contaminant.
• a "contaminant” is any substance which makes another unfit, impure or inferior.
• a purified signal-sensor polynucleotide e.g., DNA and RNA
• a quality assurance and/or quality control check may be conducted using methods such as, but not limited to, gel electrophoresis, UV absorbance, or analytical HPLC.
• the signal-sensor m NA or mmR A may be sequenced by methods including, but not limited to reverse-transcriptase-PCR.
• the signal-sensor mRNA or mmRNA may be quantified using methods such as, but not limited to, ultraviolet visible spectroscopy (UV/Vis).
• UV/Vis ultraviolet visible spectroscopy
• a non- limiting example of a UV/Vis spectrometer is a NANODROP® spectrometer (ThermoFisher, Waltham, MA).
• the quantified signal-sensor mRNA or mmRNA may be analyzed in order to determine if the signal-sensor mRNA or mmRNA may be of proper size, check that no degradation of the signal-sensor mRNA or mmRNA has occurred.
• Degradation of the signal-sensor mRNA and/or mmRNA may be checked by methods such as, but not limited to, agarose gel electrophoresis, HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC- HPLC), liquid chromatography-mass spectrometry (LCMS), capillary electrophoresis (CE) and capillary gel electrophoresis (CGE).
• HPLC based purification methods such as, but not limited to, strong anion exchange HPLC, weak anion exchange HPLC, reverse phase HPLC (RP-HPLC), and hydrophobic interaction HPLC (HIC- HPLC), liquid chromatography-mass spectrometry (LCMS), capillary electrophoresis (CE) and capillary gel electrophoresis (CGE).
• the signal-sensor primary constructs or mmRNA may also encode additional features which facilitate trafficking of the polypeptides to therapeutically relevant sites.
• One such feature which aids in protein trafficking is the signal peptide sequence.
• a "signal sequence” or “signal peptide” is a polynucleotide or polypeptide, respectively, which is from about 9 to 200 nucleotides (3-60 amino acids) in length which is incorporated at the 5' (or N-terminus) of the coding region or polypeptide encoded, respectively. Addition of these sequences result in trafficking of the encoded oncology- related polypeptide to the endoplasmic reticulum through one or more secretory pathways. Some signal peptides are cleaved from the protein by signal peptidase after the proteins are transported.
• Table 5 is a representative listing of signal proteins or peptides which may be incorporated for encoding by the signal-sensor polynucleotides, primary constructs or mmRNA of the invention. Table 5. Signal Peptides
• SS secretion signal
• MLS mitochondrial leader signal.
• the signal-sensor primary constructs or mmRNA of the present invention may be designed to encode any of the signal peptide sequences of SEQ ID NOs 94-155, or fragments or variants thereof. These sequences may be included at the beginning of the oncology-related polypeptide coding region, in the middle or at the terminus or alternatively into a flanking region. Further, any of the signal-sensor polynucleotide primary constructs of the present invention may also comprise one or more of the sequences defined by SEQ ID NOs 32-93. These may be in the first region or either flanking region.
• Additional signal peptide sequences which may be utilized in the present invention include those taught in, for example, databases such as those found at http://www.signalpeptide.de/ or http://proline.bic.nus.edu.sg/spdb/. Those described in US Patents 8,124,379; 7,413,875 and 7,385,034 are also within the scope of the invention and the contents of each are incorporated herein by reference in their entirety.
• the signal-sensor polynucleotide, primary constructs or mmRNA may include a nucleic acid sequence encoding a nuclear localization signal (NLS) and/or a nuclear export signal (NES).
• NLS nuclear localization signal
• NES nuclear export signal
• a signal-sensor may include a nucleic acid sequence encoding a nuclear export signal (NLS) and/or a nuclear export signal (NES).
• polynucleotide, primary constructs or mmRNA may include a nucleic acid sequence encoding a nuclear localization signal (NLS).
• the signal-sensor polynucleotide, primary construct or mmRNA encoding a NLS would be able to traffic an oncology related polypeptide into the nucleus and deliver a survival or death signal to the nuclear microenvironment.
• the signal-sensor polynucleotide, primary constructs or mmRNA may include a nucleic acid sequence encoding a nuclear export signal such as NES1 and/or NES2.
• the signal-sensor polynucleotide, primary constructs or mmRNA may encode a NES1, NES2 and a NLS signal and an oncology related polypeptide or a scambled sequence which is not translatable in order to interact with HIF1 -alpha to alter the transcritome of the cancer cells.
• the signal-sensor primary constructs comprise at least a first region of linked nucleosides encoding at least one oncology- related polypeptide of interest.
• the oncology-related polypeptides of interest or "targets" or oncology-related proteins and oncology-related peptides of the present invention are listed in Table 6, Table 7 and Table 41.
• Oncology-related polypeptides may be divided into classes based on their function and area of cancer intervention. For example, the classes may include targets associated with (1) apoptosis or Survival signal imbalance (AS targets).
• AS targets apoptosis or Survival signal imbalance
• ENSEMBL Transcript ID (ENST)
• ENSEMBL Protein ID (ENSP)
• OPT optimized sequence ID
• AS refers to targets involved in apoptotic signaling
• M refers to targets involved in metabolic processes
• CC/S refers to targets involved in cell cycle and senescense.

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