Patent Grant
10640539
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Feb. 18, 2019, is named 0147NF2016_US-Div Sequence Listing_ST25.txt and is 17,150 bytes in size.
The present invention provides methods useful for the delivery of protein-based complex containing silencer RNA to target cells or tissues of the brain. The invention can be used to deliver pharmaceuticals to cross the blood-brain barrier in a non-invasive manner to deliver non-toxic biological complex to decrease levels of toxic substances generated in subjects leading to neurodegenerative diseases.
Short interfering RNAs (siRNA) as gene-specific therapeutic molecules are resourceful tools to accurately control gene expression. However, delivery of these molecules to specific tissues is confronted due to their anionic nature, large size and non-specific effects preventing their clinical utility. Additionally, the delivery of siRNA to the brain parenchyma is restricted by the blood-brain barrier hampering treatment of subjects experiencing neurodegenerative conditions having long-term effects. To overcome these limitations while exploring for selectivity and non-toxicity, many peptide carriers were earlier established by conjugating antibody ligands and fusion proteins to nanoparticles through genetic engineering approaches, with the objective of targeting transferrin and insulin receptors of endothelial cells lining the brain capillaries. In a prominent advancement, different from these studies, numerous cell-targeting peptides were chosen through phage display by virtue of inherent tropism, increased avidity to mammalian cell surface receptors and ease of production. In an equivalent strategy, peptides with the binding characteristics of tetanus toxin to trisialoganglioside GT1b led to the discovery of a 12-aa peptide Tet1, offering the possibility of conjugating short peptides to larger protein scaffolds to generate multi-functional fusion proteins with neuronal tropism. Succeeding these studies, in a similar effort, Georgieva et al. developed strategies to conjugate neurotropic peptides to lipid-based molecules to impart in vivo stability, which demonstrated remarkable transcytotic capacity in vitro suggesting an identical mechanism in vivo. Upon systemic delivery, the targeting molecules, having affinity for GM1, were found to localize in the brain parenchyma and additionally in the lungs mandating further explorations to understand the potential of derivatized polymers displaying broad selectivity. Majority of non-viral vectors for nucleic acid delivery were earlier developed using the cationic lipids, cationic cell-penetrating peptides, and dendrimers. Spontaneous interaction of these molecules with nucleic acids led to the formation of stable non-covalent complexes. Knowledge-based rational design strategies subsequently led to the usage of multiple components for superior delivery and stability leading to successful target-specific gene silencing. Taking cues from neurotropic viruses, Kumar et al., fused the arginine peptide (9-mer) to a peptide derived from rabies virus glycoprotein (RVG) to facilitate electrostatic interaction with siRNA and specifically target acetylcholine receptors. The synthetic peptide fusion RVG-9R facilitated transvascular delivery of siRNA resulting in target specific gene silencing. However, presence of high density cationic charge on the carrier could lead to the formation of heterogeneous particles, non-specific biodistribution and lower yield of protein in suitable host systems.
RNA-recognition motifs conserved among double-stranded RNA-binding proteins lend their attributes to the design of modular fusion proteins. In a study using an arginine-rich peptide, tandem repeats of TAT was fused to the double-stranded RNA Binding Domain (DRBD) to electrostatically bind siRNA. The approach, although facilitating the delivery of siRNA into several primary cells including glioma lacked cell-specificity. It is thus evident that multiple DRBD motifs fused with cationic peptides may not confer additional in vivo advantage due to their likely interaction with serum proteins, lack of target selectivity and tendency to aggregate. Versatility of TARBP2 fusion protein whose conformation-dependent binding to double-stranded RNA abolished the prerequisite of positively charged peptides. The strong binding interactions led to the formation of neutral nanosized complex which were stable upon systemic administration. In the present invention, we have overcome the aforesaid barriers and invented a method to deliver siRNA selectively to target the brain and central nervous system, by fusing the RNA-binding domain with a peptide having sequence GGGGHLNILSTLWKYRC represented by SEQ ID NO. 9 that can retain flexibility and at the same time target GM1 and GT1b expressing cells, by virtue of their natural abundance of these receptors in neuronal cells to permit accumulation of the silencer complex with the aim of targeting disease causing genes in neurodegenerative condition by the advantage and ability of the peptide chimera to cross the blood-brain barrier by receptor-mediated transcytosis by mediating efficient and effective RNAi via GM1 in brain tissue.
The main objective of the present invention is to provide a method of preparation of a protein based complex comprising silencer RNA [siRNA] for target specific delivery to a ganglioside.
Another objective of the present invention is to provide a method for target specific delivery of a protein based complex comprising silencer RNA [siRNA] to a ganglioside.
Yet another objective of the present invention is to provide a protein based complex comprising silencer RNA [siRNA] for target specific delivery to a ganglioside by receptor mediated transcytosis.
An objective of the present invention is to provide a method of treating diseases selected from the group consisting of alzheimer's, parkinsons, gliomas, and amyotrophic lateral sclerosis which comprises administering to a subject an effective amount of protein based complex comprising silencer RNA [siRNA].
The present invention describes a method of preparation of a protein based complex comprising silencer RNA [siRNA] for target specific delivery to a ganglioside, wherein said method comprises:
a) fusing RNA Binding domain [RBD] of human Trans Activation Response Element RNA Binding Protein [TARBP] with a brain targeting peptide [BTP] to form a fusion protein [TARBP-BTP];
b) cloning, overexpressing and purifying said fusion protein [TARBP-BTP] to obtain a purified fusion protein [TARBP-BTP]; and
c) associating said purified fusion protein [TARBP-BTP] with siRNA to form a protein based complex.
In an embodiment of the present invention, the ganglioside is selected from GM1 or GT1b expressing cells.
In another embodiment of the present invention, RNA Binding domain is double stranded[dsRBD].
In a further embodiment of the present invention, TARBP-BTP protein and silencer RNA is mixed in 5:1 mole ratio.
In an embodiment of the present invention, TARBP-BTP protein and silencer RNA is mixed in 2.5:1 mole ratio.
In another embodiment of the present invention, silencer RNA is BACE1 silencer RNA.
In a further embodiment of the present invention, BTP is having amino acid sequence represented by SEQ ID NO. 9.
In an embodiment of the present invention, cloning is in pET28a plasmid, over expression in E. coli BL21(DE3) cells and purification using Ni-NTA affinity chromatography.
The present invention also describes a method for target specific delivery of a protein based complex comprising silencer RNA [siRNA] to a ganglioside, wherein said method comprises the steps of:
a) fusing RNA Binding domain [RBD] of human Trans Activation Response Element RNA Binding Protein [TARBP] with a brain targeting peptide [BTP] to form a fusion protein [TARBP-BTP];
b) cloning, overexpressing and purifying said fusion protein [TARBP-BTP] to obtain a purified fusion protein [TARBP-BTP];
c) associating said purified fusion protein [TARBP-BTP] with siRNA to form a protein based complex; and
d) selectively targeting said protein based complex to the ganglioside by receptor mediated transcytosis.
In an embodiment of the present invention, ganglioside is selected from GM1 or GT1b expressing cells.
In another embodiment of the present invention, RNA Binding domain is double stranded [dsRBD].
In a further embodiment of the present invention, TARBP-BTP protein and silencer RNA is mixed in 5:1 mole ratio.
In an embodiment of the present invention, TARBP-BTP protein and silencer RNA is mixed in 2.5:1 mole ratio.
In another embodiment of the present invention, silencer RNA is BACE1 silencer RNA.
In a further embodiment of the present invention, BTP is having amino acid sequence represented by SEQ ID NO. 9.
In an embodiment of the present invention, cloning is in pET28a plasmid, over expression in E. coli BL21(DE3) cells and purification using Ni-NTA affinity chromatography.
The present invention describes a protein based complex comprising silencer RNA [siRNA] for target specific delivery to a ganglioside by receptor mediated transcytosis, wherein said complex comprises RNA Binding domain [RBD] of human Trans Activation Response Element RNA Binding Protein [TARBP] along with a brain targeting peptide [BTP] and silencer RNA.
The present invention also describes a method of treating diseases selected from the group consisting of alzheimer's, parkinsons, gliomas, and amyotrophic lateral sclerosis which comprises administering to a subject an effective amount of protein based complex comprising silencer RNA [siRNA].
These and other features, aspects, and advantages of the present subject matter will become better understood with reference to the following description and appended claims. This summary is provided to introduce a selection of concepts in a simplified form. This summary is not intended to identify key features or essential features of the claimed subject matter, nor is it intended to be used to limit the scope of the claimed subject matter.
SEQ ID NO: 1. pET28a Cloning vector (nucleic acid sequence)
SEQ ID NO: 2. TARBP-BTP nucleic acid sequence designed construct that can be expressed in Escherichia coli (nucleic acid sequence)
SEQ ID NO: 3. BTP Primer sequence: Synthetic primer designed for PCR (nucleic acid sequence)
SEQ ID NO: 4. Fg23 Primer sequence: Synthetic forward primer (nucleic acid sequence)
SEQ ID NO: 5. Rg 23 Primer sequence: Synthetic reverse primer (nucleic acid sequence)
SEQ ID NO: 6. BTP Primer sequence: synthetic primer for amplifying the brain targeting ligand for expression in Escherichia coli (nucleic acid sequence)
SEQ ID NO: 7. FBTP Primer sequence: Synthetic primer for overlap PCR (nucleic acid sequence)
SEQ ID NO: 8. Rg-23 Primer sequence: Synthetic primer for PCR (nucleic acid sequence)
SEQ ID NO: 9. BTP amino acid sequence of the targeting ligand linked to TRBP2 that can be expressed in Escherichia coli (amino acid sequence)
SEQ ID NO: 10. Homo sapiens TARBP2, RISC loading complex RNA binding subunit (TARBP2), transcript variant 1, mRNA (nucleic acid sequence)
SEQ ID NO: 11. fTRBP2: Sequence corresponding to DNA originally isolated from HeLa Cells from which RNA was isolated and used to synthesize cDNA by reverse transcriptase (nucleic acid sequence)
SEQ ID NO: 12. TARBP2 amino acid sequence: Translated amino acid sequence obtained from SEQ No: 11 (amino acid sequence)
SEQ ID NO: 13. Complete sequence of gene with Restriction site (TRBP2-CCCBTP): gene amplicon that can be generated in Escherichia coli after cloning and transformation (nucleic acid sequence)
SEQ ID NO: 14. NdeI Restriction site (nucleic acid sequence)
SEQ ID NO: 15. XhoI Restriction site (nucleic acid sequence)
SEQ ID NO: 16: TARBP-BTP complete amino acid sequence: translated amino acid sequence corresponding to the molecular weight of TARBP-BTP (amino acid sequence)
SEQ ID NO: 17. TARBP-BTP nucleotide sequence: complete amplicon after cloning and transformation of TARBP-BTP cloned in pET 28a and then transformed in Escherichia coli (nucleic acid sequence)
The invention reveals the groundwork of the functional formulation that is a simple complex comprising of purified modular TARBP-BTP protein chimera with the brain targeting ligand. The chimera is an endotoxin-free protein molecule having the ability to form a consistent and active complex with short silencer RNA bound in a conformation-specific manner. The resultant complex containing TARBP-BTP containing the silencer RNA selectively targets GM1. The targeting functionality fosters the ability to cross the blood-brain barrier and localize in the brain tissues to mediate therapeutic RNA interference (RNAi). The invention established in a mouse model reveals that following non-invasive delivery, the complex is capable of entering and localizing in brain tissues particularly the hippocampus and the cortex and to some extent the olfactory bulb and the striatum and decrease levels of toxic peptide generation in these regions. These properties are the hallmark of a therapeutic pharmaceutical for treating neurodegenerative condition additionally in other mammalian subjects.
The following examples are given by way of illustration of the present invention and should not be construed to limit the scope of present disclosure. It is to be understood that both the foregoing general descriptions and the following detailed description are exemplary and explanatory only and are intended to provide further explanation of the subject matter.
Design, Cloning Strategy by Overlap PCR and DNA Sequencing
To construct recombinant TARBP-BTP fusion, gene sequence from TRAF corresponding to the second domain (TARBP2/TRBP2) of the mammalian homolog, a linker sequence encoding five glycine residues and DNA fragment encoding the brain targeting peptide sequence together with a C-terminal cysteine codon was amplified by overlapping PCR. DNA duplexes with and without the targeting ligand were cloned in pET28a plasmid (Novagen) in the NdeI-XhoI site to generate N-terminal 6 His-tagged fusion constructs that were verified by DNA sequencing. The N-terminus-tagged fusion protein TARBP-BTP, a 13.378 kDa with the corresponding DNA and translated protein sequence by EXPASY. TARBP having high affinity to double-stranded RNA (dsRNA) was fused to a ganglioside targeting peptide sequence, originally selected by phage display for GT1b and GM1 binding to deliver siRNA to the brain.
Purification and Verification of TARBP-BTP
The selected recombinants were expressed in E. coli BL21(DE3) cells and purified to homogeneity using Ni-NTA affinity chromatography. E. coli BL21(DE3) cells overexpressing the recombinant proteins were lysed under denaturing conditions using lysis buffer (50 mM sodium phosphate buffer pH 7.4 containing 300 mM NaCl, 10 mM Tris, 6 M urea and 1 mM PMSF) followed by sonication. Following centrifugation of the lysate at 18,000 rpm for 20 min to pellet cell debris, the supernatant was incubated with the pre-equilibrated Ni-NTA sepharose matrix for 1 h. The matrix was then loaded onto a column and washed with 0.1% Triton X-114 in lysis buffer at 4° C. to remove the bacterial endotoxins. The matrix bound TARBP-BTP protein was refolded under native conditions by on-column refolding and eluted using sodium phosphate buffer (pH 7.4) containing 300 mM imidazole. The eluted fractions were pooled, desalted and buffer exchanged in phosphate buffered saline (PBS) pH 7.4 using Sephadex G25 superfine column and purity and quality validated by western blotting and mass spectrometry.
Far UV CD Spectrum
Far UV CD spectrum (range 250-200 nm) of purified TARBP-BTP (0.1 mg/ml in PBS (pH 7.4) recorded at room temperature using JASCO-J-815 spectropolarimeter equipped with Jasco Peltier-type temperature controller (CDF426S/15). The secondary structure analysis of TARBP-BTP by CD spectroscopy reveals that the secondary structure of the silencer-binding domain is unaltered. The spectrum, acquired in a 1 cm path length cuvette, was an average of five scans that was corrected for the buffer baseline and plotted using Origin? software (OriginLabCorp.). Spectra were recorded in ellipticity mode at a scan speed of 50 nm/min, response time of 2 s, bandwidth of 2 nm and data pitch of 0.2 nm. Mean residual ellipticity was calculated as described. Further, far-UV circular dichroism spectroscopy suggested a well-defined secondary structure, consisting of both α-helices and β-pleated sheets similar to earlier observations.
Ability of Complex to Bind and Protect Silencer RNA (siRNA)
The complex was prepared by incubating 20 pmol of siRNA to increasing concentrations of TARB-BTP fusion protein in PBS buffer to obtain the preferred mole ratios and incubated for 20 min prior to electrophoresis. For the protection assay, the complex with and without the targeting ligand were incubated for 20 min followed by treatment with RNase A for 1 h at 37° C. Samples were then extracted by phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated using ethanol as described previously and resolved by gel electrophoresis. The stability of TARBP-BTP and TARBP complex was further assessed by preparing the complex in PBS or DMEM media plus 10% serum followed by incubation for 1-6 h at 37° C. siRNA was then extracted by phenol-chloroform and resolved on 2% agarose gel and visualized by ethidium bromide staining. siRNA alone and TARBP-BTP or TARBP alone loaded in separate lanes serve as controls. Binding of the fusion protein to siRNA indicated strong association and formation of homogenous non-covalent complex that upon electrophoresis indicated strong binding and near-complete masking of siRNA at 2.5:1 mole ratio with maximal binding at 5:1 mole ratio. At these ratios, the complex was resistant to degradation by RNase A and this ratio was used to prepare the functional complex for the in vitro and in vivo experiments. Out data reflects the ability of recombinant his-tagged TARBP-BTP and his-tagged TARBP protein to bind dsRNA in a conformation-specific manner, an attribute essential for in vivo stability of the carrier upon delivery.
TARBP-BTP Complex Binds Ganglioside GM1 and Internalized by Cells In Vitro
The complex was prepared at 5:1 mole ratio, since maximal binding and protection of siRNA was observed. Complex added to Neuro-2a, IMR32 and HepG2 cells in culture exhibiting varying levels of GM1 also depicted entry into cells via GM1 on the cell surface. This was supported in a FACS-based uptake assay evaluated in Neuro-2a, IMR32 and HepG2 cells using FAM-labeled siRNA complexed with TARBP-BTP. In such a condition, 59.76%, 40.4% and 7.92% of cells respectively were found to be FAM-positive clearly indicating that uptake is GM-1 dependent.
In Vitro Functional Knockdown of TARBP-BTP:siRNA Complex
Delivery of BACE1 silencer RNA in GM1-rich Neuro-2a cells. Knockdown assay using qRT-PCR in Neuro-2a cells, having the highest levels of GM1 depicted that TARBP-BTP led to 41% knockdown of BACE1 mRNA levels.
Non-Toxicity of the Complex TARBP-BTP:siRNA In Vitro
In the drawings accompanying the specification, the complex was non-toxic to cells when evaluated in an MTT cell-viability assay, which indicated ˜90% viability at all the ratios examined. Cells were treated with TARBP-BTP:siRNA complex for 24 h and assessed in the presence and absence of siRNA at the indicated mole ratios using MTT. Cells treated with PBS alone were considered as controls having 100% viability from absorption values measured using reduced formazan. Error bars indicate standard deviation of triplicate sets.
Biodistribution of the Complex In Vivo Upon Intravenous Delivery in AD Mice
Firstly, for the preparation of the protein complex comprising of silencer RNA and TARBP-BTP fusion protein was prepared in 1×PBS pH 7.4. The purified protein solution is then filtered using 0.22 mm Milex filters to get rid of any microbes and protein aggregates if any. The required amount of siRNA is also diluted in 1×PBS pH 7.4. Complexes are formed by mixing solutions of protein and siRNA in equal volumes eg. 100 ml of protein and 100 ml of siRNA (the concentrations are adjusted in such a way that the mole ratio is always kept at 5:1 protein:siRNA). Following the mixing, the solution is incubated at 4° C. for 15 min (incubation at RT may lead to the formation of aggregates). This complex (200 ml) is injected via the tail vein in mice using standard protocols of delivery. In the drawings accompanying the specification, the distribution of fluorescent complex (TARBP-BTP:siRNA) in AβPP-PS1 mouse brain upon intravenous delivery demonstrated its in vivo potential to cross the blood-brain barrier. This was executed by administering fluorescent complex that were prepared by mixing corresponding amounts of fluorescent-TARBP-BTP and silencer RNA at 5:1 mole ratio. Mice injected with the same volume of PBS served as negative controls. Mice were euthanized 6 h post-delivery of the complex and all the major organs, including brain were dissected, sectioned and visualized. Even though AF633 signal originating from the labeled protein enabled collection of fluorescent signals in the far-red spectrum with minimum background noise, non-specific fluorescence arising from all laser lines in the brain sections was eliminated by NaBH4 and CuSO4 treatment of tissue sections as described in the methods. In the representative brain sections of mice injected with Alexa Fluor633-TARBP-BTP:siRNA complex, the localization of fluorescent complex is distinctly visible in the cerebral cortex and the hippocampus region (boxed area), which clearly indicates transcytosis of the complex across the blood-brain barrier. To authenticate that the observed signal arising from the 633 nm laser line is from the labeled protein, the emission spectrum was matched with that of AF633-TARBP-BTP fusion protein spotted separately on a coverslip, using lambda scan option in Leica SP8. In contrast, the lack of fluorescence in the lung, liver and intestine and other organs such as the heart and spleen indicated target specificity of TARBP-BTP. Fluorescence depicted in a different region of the brain i.e. brain cortex, is shown in Representative sections stained with CD31 mark the endothelial cells of the brain capillaries. Significant Alexa Fluor633 fluorescence originating from kidney tissue sections indicated excretion of the labeled complex through renal filtration.
Therapeutic Delivery of AD-Relevant Silencer Complex In Vivo in AD Mice and C57BL/6 Wild Type Mice
The role of BACE1 in the cleavage of amyloid precursor protein (APP) and consequent generation of Aβ peptide is known. Complex comprising TARBP-BTP and BACE1 silencer RNA at 5:1 mole ratio was intravenously delivered. Both AβPP-PS1 and C57BL/6 mice were injected with the complex intravenously and evaluated 48 h post administration by qRT-PCR and western blotting. In addition to PBS control, naked BACE1 silencer RNA and TARBP-BTP complexed with non-targeting control silencer RNA were also injected into C57BL/6 mice.
In vivo experiments with BACE1 siRNA delivery mediated by TARBP-BTP clearly establish i) the in vivo stability, ii) tissue-specific targeting across the blood-brain barrier and prominently iii) region specificity of TARBP-BTP:siRNA complex in successfully delivering BACE1 validated silencer RNAs bound to the carrier complex. The functional complex comprising the bi-functional chimeric peptide and BACE1 silencer RNA, a therapeutically relevant AD gene, would be capable of mediating therapeutic effects by the ability to cross the blood-brain barrier and enter the brain tissues particularly in sites of learning and memory to knockdown expression of the products responsible for generating toxic peptides. The method is useful for targeting neurodegenerative diseases, e.g. AD and will find therapeutic applications in the central nervous system for other diseases.
Additionally, TARBP-BTP will be useful for functional analysis of hitherto unknown genes. The delivery system due to conformation-specific binding of the silencer offers a robust complex whose serum stability and controlled release in target tissues in a non-toxic and non-immunogenic manner will find utility in clinical applications.
This application is a Divisional of U.S. patent application Ser. No. 15/266,642 filed on Sep. 15, 2016, now U.S. Pat. No. 10,209,098, issued Feb. 19, 2019. The entire contents of this application is incorporated herein by reference in its entirety.
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| 10329569 | Kim | Jun 2019 | B2 |
| 10398784 | Mirkin | Sep 2019 | B2 |
| 20060030003 | Simon | Feb 2006 | A1 |
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| Number | Date | Country | |
|---|---|---|---|
| 20190309032 A1 | Oct 2019 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15266642 | Sep 2016 | US |
| Child | 16278319 | US |
