Compositions and systems comprising transfected active vesicles free of organic solvents and detergents and methods related thereto

Abstract

The present application relates to methods of encapsulating selected cargo in lipid-transfected active vesicles (TCVs). Lipid-based vesicles, typically referred to herein as transfection active vesicles (TCVs), are configured to safely and efficiently deliver DNA, RNA, other nucleic acids and protein cargo into target cells. One and both of safety and efficiency are achieved in part by eliminating an organic solvent (e.g., ethanol) and a detergent (e.g., lauryl sodium sulfate) from a TCV loading process (i.e., cargo insertion into the TCV), a TCV storage process, and / or a TCV delivery process. The cargo may also comprise a nucleic acid complexed with a protein (e.g., ribonucleoprotein (RNP)). In some embodiments, the systems, compositions, devices, and methods described herein all can provide the desired empty TCV that can be table-loaded without the use of specialized equipment.

Description

This application is a divisional application of the Chinese patent application with application number 201980065376.1. CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of co-pending U.S. Provisional Patent Application Serial No. 62 / 743,116, filed on October 9, 2018, which is incorporated herein by reference in its entirety. Background Art

[0002] One of the important fields of scientific research and medical treatment is to hope to selectively and effectively deliver RNA, DNA, other nucleic acids and / or protein cargo to target sites, such as specific target cells. For many reasons, this may be helpful, including improving patient treatment (such as gene therapy) and for treating cancer and other conditions. For example, gene therapy may be able to be used for the brain and the entire central nervous system to treat some typical terrible neurological disorders that humans may suffer from, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, frontotemporal dementia, amyotrophic lateral sclerosis, spinal muscular atrophy, etc. There are several problems in the current gene therapy method while it is widely used, particularly for human patients, such as because it is necessary to carry the therapeutic nucleic acid to the repeated use and toxicity of the packaging in the patient's body. Current compositions, methods, etc. described herein help to solve one or more of these problems or other such problems.

[0003] For more scientific discussions about DNA and other nucleic acids being delivered to target sites (e.g., diseased cells in the brain), existing methods for such delivery include lipid particles, which are referred to as lipid nanoparticles ("LNPs") or liposomes in some cases. The term lipid nanoparticle or "LNP" is used to describe lipid-based particles at approximately neutral pH, which typically contain nucleic acids and have an electron-dense core. Liposomes, also referred to as vesicles, are lipid-based structures with a single double layer and an aqueous core. The typical known method for LNP formation is to load specific cargo into the vesicle when the initial vesicle is formed. These methods further use specialized instruments, organic solvents and / or detergents, require a large amount of material and include processing times of several days, all of which severely hinder practicality, accessibility, and therapeutic availability.

[0004] LNPs and other lipid particles typically contain an ionizable cationic lipid, one or more phospholipids, cholesterol (Chol), and polyethylene glycol-lipid (PEG-lipid) (Maurer, Wong et al., 2001; Semple, Klimuk et al., 2001; Semple, Akinc et al., 2010; Belliveau, Huft et al., 2012; Leung, Hafez et al., 2012; Suhr, Coelho et al., 2015). (Various references are listed herein that discuss certain systems, devices, methods, and other information; all of these references are incorporated herein by reference in their entirety and include all of their teachings and disclosures, regardless of where the references may appear in this application. Citation of a reference herein is not an admission that such reference constitutes prior art to the present application.) An example of an LNP composition is a combination of an ionizable cationic lipid, a phospholipid, cholesterol, and polyethylene glycol (PEG)-lipid (respectively) in a ratio of 50 / 10 / 38.5 / 1.5 mol%. This composition has been shown to exhibit effective hepatocyte gene silencing (siRNA) or expression (mRNA) after intravenous administration (Semple, Akinc et al., 2010; Jayaraman, Ansell et al., 2012; Pardi, Tuyishime et al., 2015; Suhr, Coelho et al., 2015). Others have described LNP compositions composed of ionizable cationic lipids, phospholipids, cholesterol, and polyethylene glycol (PEG)-lipids in a ratio of 50 / 10 / 38.5 / 1.5 mol % as siRNA delivery to primary neuronal cells in culture and for delivery to the brain (Rungta, Choi et al., 2013).

[0005] LNP formulations can be produced by rapid mixing of a lipid component dissolved in ethanol and an acidic aqueous phase consisting of the nucleic acid cargo (Jeffs, Palmer et al., 2005; Belliveau, Huft et al., 2012; Leung, Hafez et al., 2012). Established rapid mixing methods for LNP preparation include microfluidic mixing via a staggered herringbone micromixer (SHM) (Belliveau, Huft et al., 2012; Rungta, Choi et al., 2013; Leung, Tam et al., 2015), or T-junction mixing with dedicated pumps (Jeffs, Palmer et al., 2005) or the more outdated ethanol / detergent-destabilized loading of preformed vesicles (Wheeler, Palmer et al., 1999; Tam, Monck et al., 2000; Maurer, Wong et al., 2001; Semple, Klimuk et al., 2001). In all three methods, ethanol solutions (or detergents) are required to provide sufficient membrane fluidity for lipid reorganization and encapsulation, and in the case of SHM and T-junction techniques, particle formation also occurs when the ethanol solution is diluted into the aqueous phase (Belliveau, Huft et al., 2012; Zhigaltsev, Belliveau et al., 2012; Zhigaltsev, Tam et al., 2016). However, due to the organic solvents and acidic pH, the resulting suspension is not "ready to use", and therefore the resulting suspension requires extensive downstream processing. In terms of material cost and time, these methods have obvious obstacles to achieving transfection-active preparations at laboratory scale for in vitro applications or at therapeutic levels for direct administration.

[0006] There remains a need for transfection reagents that effectively deliver nucleic acid and protein cargoes into mammalian cells in a non-toxic manner, including for use in cultured mammalian primary cells (generally, primary cells are non-transformed, non-immortalized cells obtained directly from target tissues). While the importance of using primary cells and their advantages over using cell lines are well understood, the difficulties encountered in transfecting such cells have almost completely precluded their use for any type of discovery or validation studies requiring selective gene knockdown. In addition, the move toward personalized medicine is driving functional genomic screening and validation in primary patient cells, increasing the need for robust and non-toxic transfection methods for these difficult-to-transfect cell types.

[0007] The systems and methods of the present invention, among other things, provide solutions that address one or more of these difficulties and / or provide other advantages. Summary of the invention

[0008] The systems, compositions, devices, methods, etc. described herein provide lipid-based vesicles, generally referred to herein as transfection-competent vesicles (TCVs), which are configured to safely and efficiently deliver proteins, ribonucleoproteins (RNPs), RNA, DNA, and other nucleic acid cargoes, as well as other selected cargoes, to target cells. One or both of safety and efficiency are achieved in part by eliminating destabilizing agents (e.g., organic solvents (e.g., ethanol) and detergents (e.g., sodium dodecyl sulfate)) from the TCV loading process (i.e., inserting the selected cargo into the TCV), the TCV storage process, and / or the TCV delivery process. Thus, the TCV is maintained in a destabilizing agent-free solution, for example, as a destabilizing agent-free suspension.

[0009] As used herein, TCV is a liposome or other lipid-based vesicle, and is produced and / or stored in the absence of a destabilizer and the absence of a selected cargo inside. An advantage of this TCV is that they can be stored in solution or as a suspension in the absence of a destabilizer, and can encapsulate selected cargo in the absence of a destabilizer, and such selected cargo can be delivered to target cells in the absence of a destabilizer. The selected cargo refers to RNP, RNA, DNA, protein, etc., which produces the desired effect on target cells and / or target patients transfected with TCV containing the selected cargo. Therefore, unless the context clearly indicates otherwise, the TCV described herein lacks the final selected cargo, and in certain embodiments is empty except for the environmental solution, etc. Such TCV is configured to safely and effectively deliver nucleic acids and protein cargoes, etc. to mammalian cells without the use of organic solvents or other destabilizers.

[0010] The TCV delivery method may include transfecting mammalian cells (e.g., primary cells) with a selected cargo. The cargo may also include nucleic acids complexed with proteins, such as ribonucleoproteins (RNPs). In some embodiments, the systems, compositions, devices, methods, etc. described herein may provide an empty TCV or a loaded TCV.

[0011] In some aspects, the systems, compositions, devices, methods, etc. described herein provide transfection-active vesicles (TCVs) that do not contain organic solvents and other destabilizing agents that were previously required to encapsulate (or load) cargo into lipid vesicles or liposomes and / or store these vesicles. The compositions, methods, etc. described herein can be used or performed without the use of specialized instruments, for example, the prefabricated TCVs herein can be loaded by gently mixing a suspension containing empty TCVs with various types of selected cargoes through reciprocating motions of a pipette. The compositions, methods, etc. described herein are particularly suitable for "benchtop loading" and can be used with small or large amounts of selected cargo materials. In addition, a single batch of empty TCVs can be bench-loaded with a variety of different selected cargoes in parallel.

[0012] In some embodiments, the systems, compositions, devices, methods, etc. described herein provide an empty TCV that is free of organic solvents and free of detergents. If ethanol or detergents or other destabilizing agents have been used to form the TCV, they are removed by dialysis or other suitable methods to provide an organic solvent-free, detergent-free TCV composition. The TCV can be loaded using gentle mixing (e.g., repeated manual reciprocating motion of the TCV-generating fluid in a pipette), SHM, T-junction mixing or extrusion methods, or other TCV mixing methods as desired.

[0013] In one aspect, the lipid-based TCV is composed of a mixture of ionizable cationic lipids, phospholipids, cholesterol, and PEG-lipids, and the composition comprising the TCV is free of organic solvents and / or detergents, such terms being used in their normal usage to mean the substantial absence of such organic solvents and detergents, such that the organic solvents and / or detergents do not cause significant deleterious effects, although small trace amounts may remain in the composition.

[0014] In some aspects, the ionizable cationic lipid comprises 20-50% of the lipid component of the TCV. On the one hand, the empty lipid-based TCV contains a lipid component of DODMA / DOPE / DSPC / Chol / PEG-lipid in a ratio of 20 / 30 / 10 / 39 / 1mol%. On the other hand, the empty lipid-based TCV contains a lipid component of DODMA / DOPE / DSPC / Chol in a ratio of 20 / 30 / 10 / 40mol%. On the other hand, the empty lipid-based TCV contains a lipid component of DODMA / DOPE / DSPC / Chol / PEG-lipid in a ratio of 50 / 10 / 39 / 1mol%. On the other hand, the empty lipid-based TCV contains a lipid component of DODMA / DOPE / DSPC / Chol in a ratio of 50 / 10 / 39 / 1mol%. Various other components may also be used as needed. In some aspects, the proportion of ionizable cationic lipids is reduced. For example, the proportion of the ionizable cationic lipid may be about 10 mol%, 20 mol%, 30 mol%, 40 mol%, 50 mol% or 60 mol%.

[0015] In one aspect, the empty lipid-based TCV is mixed with the nucleic acid-based selected cargo for 5 seconds, 10 seconds, 15 seconds, 20 seconds, 30 seconds, 45 seconds, 1 minute or 2 minutes, such as 10-30 seconds, as desired. The organic solvent-free, detergent-free TCV can then be stored in an organic solvent-free, detergent-free environment and / or administered to a target cell (e.g., a mammalian cell) again in an organic solvent-free, detergent-free environment.

[0016] In some aspects, the nucleic acid type selected goods can be double-stranded DNA, single-stranded DNA, RNA, small interfering RNA, short hairpin RNA, messenger RNA, complementary DNA, microRNA, plasmid DNA or a combination thereof. In some aspects, the nucleic acid type selected goods can include synthetic or chemically modified oligonucleotides, such as to improve the stability of the selected goods. The selected goods can be a protein (PNA) compounded with nucleic acid. The protein type selected goods can be a protein involved in gene editing or a protein (such as a fluorescent marker, etc.) used as a reporter molecule for cell labeling. In some embodiments, the protein-based selected goods compounded with nucleic acid are ribonucleoproteins.

[0017] In some aspects, the systems, devices, methods, etc. of the present invention provide a method for encapsulating a selected cargo into a lipid-based transfection-competent vesicle (TCV), comprising: - providing a water-based solution comprising a lipid-based TCV, wherein the water-based solution may be free of a destabilizing agent; as well as, - mixing the selected cargo into a solution under suitable conditions and for a sufficient time to allow the selected cargo to be encapsulated within the lipid-based TCV to provide a lipid-based TCV-encapsulated selected cargo, wherein the mixing is performed in the absence of an organic solvent or detergent.

[0018] The destabilizer can be at least one of an organic solvent or a detergent. The organic solvent can be, for example, methanol, isopropanol, tetrahydrofuran (THF), dimethyl sulfoxide (DMSO), dimethylformamide (DMF) or acetonitrile (ACN). The detergent can be, for example, sodium dodecyl sulfate (SDS). The destabilizer can be temperature. The aqueous solution can be 25 mM to 100 mM acetate buffer.

[0019] The lipid-based TCV may be empty prior to encapsulation, and the method may further comprise: - Obtain lipid-based TCV encapsulation of selected cargo in an aqueous solution substantially free of solvents and detergents.

[0020] The lipid-based TCV may comprise a cationic lipid, such as an ionizable cationic lipid. The lipid-based TCV may comprise about 20 mol% to 50 mol% of a cationic lipid. The ionizable cationic lipid may comprise 1,2-dioleyloxy-3-dimethylamino-propane (DODMA). The lipid-based TCV may comprise a mixture of 1,2-dioleyloxy-3-dimethylamino-propane (DODMA), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC). The mixture may also comprise at least one of polyethylene glycol (PEG) or cholesterol.

[0021] The lipid-based TCV may comprise a mixture of about 20 / 30 / 10 / 39 / 1 mol % DODMA / DOPE / DSPC / Chol / PEG-lipid, may comprise a mixture of about 20 / 30 / 10 / 40 mol % DODMA / DOPE / DSPC / Chol, a mixture of about 50 / 10 / 40 mol % DODMA / DSPC / Chol, a mixture of about 50 / 10 / 39 / 1 mol % DODMA / DSPC / Chol / PEG-lipid, or a mixture of about 50 / 10 / 39 / 1 mol % DODMA / DSPC / Chol / PEG.

[0022] The selected cargo can be a nucleic acid, such as a modified nucleic acid. The modified nucleic acid can include, for example, at least one of 2'-O-methylation (2'-O-ME), phosphorothioate or morpholino nucleic acid, locked nucleic acid. The nucleic acid can be a deoxyribonucleic acid (DNA). The DNA can include double-stranded DNA, single-stranded DNA, complementary DNA (cDNA) or plasmid DNA. The nucleic acid can include ribonucleic acid (RNA). The RNA can include small interfering RNA (siRNA), short hairpin RNA, messenger RNA (mRNA), microRNA (miRNA). The selected cargo can include a protein. The protein can be part of a ribonucleoprotein (RNP), which can be a functional ribonucleoprotein. The RNP can include at least one of a Cas9 protein or a guide RNA, both a Cas9 protein and a guide RNA, or a Cas9 protein and a guide RNA and a single-stranded DNA (ssDNA).

[0023] The cargo may comprise at least one of an enzyme, a nuclease, and an endonuclease or a primer. The cargo may comprise at least one of a zinc finger nuclease (ZFN), a TALEN, Cas9, Cas10, Cas11, Cas12, or Cpf1. The cargo may comprise at least one of an enzyme, a nuclease, and an endonuclease or a primer. The cargo may comprise mRNA encoding a nuclease or an antigen.

[0024] The method may also include mixing a lipid-based TCV with a selected cargo, which may be a nucleic acid, present in a ratio of about 0.022-0.058 mg of the selected cargo per micromole of cationic lipid. The method may also include mixing a lipid-based TCV with a selected cargo, which may be a nucleic acid, present in a ratio of about 0.029-0.116 mg of the selected cargo per micromole of cationic lipid. The lipid-based TCV and the selected cargo may be mixed with a lipid-based TCV:selected cargo at a molar ratio of about 467. The selected cargo may be a ribonucleoprotein (RNP). The lipid-based TCV and the selected cargo may be mixed with a lipid-based TCV:selected cargo at a molar ratio of about 400 to 1200. The lipid-based TCV and the selected cargo may be mixed with a lipid-based TCV:selected cargo at a molar ratio of about 473 to 1173. The lipid-based TCV and the selected cargo may be mixed with a lipid-based TCV:selected cargo at a molar ratio of up to about 3000 to 5000.

[0025] The lipid-based TCV and the selected cargo can be mixed at about room temperature for about 10 to 15 seconds, or about 10 to 30 seconds. Mixing can be performed using staggered herringbone micromixing or T-junction mixing. Mixing can be performed by a reciprocating motion in a pipette.

[0026] In some aspects, the systems, devices, methods, etc. of the present invention provide a composition comprising a lipid-based transfection-active vesicle (TCV) in an aqueous solution. The composition may be free of destabilizing agents (organic solvents and detergents). The composition and / or lipid-based TCV may also be configured as discussed in the "Summary of the Invention", "Drawings" and "Detailed Description of the Invention" or "Claims". The systems, devices, methods, etc. of the present invention provide a composition comprising a lipid-based transfection-active vesicle (TCV) encapsulated selected cargo in an aqueous solution, which is substantially free of destabilizing agents (e.g., organic solvents and detergents). As discussed herein, the lipid-based TCV encapsulates the selected cargo.

[0027] The systems, devices, methods, etc. of the present invention also provide a transfection method, comprising transfecting a target cell with a selected cargo encapsulated by a lipid-based transfection-activated vesicle (TCV) as discussed herein. The target cell can be a mammalian cell, such as a primary mammalian cell, a primary mammalian neuronal cell, a cultured mammalian cell, or a cell from a mammalian patient.

[0028] The methods described herein can be performed in a laboratory, e.g., for benchtop loading. The methods can be performed in a factory to produce commercial quantities of transfected cells. The methods can be performed as part of an in vivo procedure, a medical procedure, a therapeutic procedure, or a gene therapy procedure. The methods can be performed as part of treating Alzheimer's disease, Parkinson's disease, Huntington's disease, frontotemporal dementia, amyotrophic lateral sclerosis, or spinal muscular atrophy. The methods can also include delivering the selected cargo encapsulated by the lipid-based TCV to the patient's brain.

[0029] In some other aspects, the systems, devices, methods, etc. of the present invention provide a kit comprising the composition of the present invention. The composition can be in a container and the kit can include instructions for use of the composition. The instructions can guide the use of the composition according to any method of the present invention. The container can be configured to administer at least one dose of the composition to a mammal, and the kit further comprises at least one label comprising instructions for administration.

[0030] In some aspects, the systems, devices, methods, etc. of the invention provide isolated and purified compositions herein for use in the preparation of a medicament for inhibiting, preventing or treating a disease or condition in a patient (which may be a mammal).

[0031] These and other aspects, features, and embodiments are described in the present application, including the following detailed description and accompanying drawings. Unless otherwise expressly stated, all embodiments, aspects, features, etc. may be mixed and matched, combined, and arranged in any desired manner. In addition, various references discussing certain systems, devices, methods, and other information are listed herein, including in the "Cross-References to Related Applications"; all of these references are incorporated herein by reference in their entirety and include all of their teachings and disclosures, regardless of where the references may appear in this application. BRIEF DESCRIPTION OF THE DRAWINGS

[0032] Figure 1A-1D shows that transfection active vesicles (TCVs) produced according to the methods herein show knockdown in immortalized cells and primary neurons. (A) Relative luciferase expression in HEK-Luc cells after transfection with organic solvent-free, detergent-free TCVs composed of 50% ionizable cationic lipids. (B) Cell viability from the same transfection group presented in (A) as a percentage of the control (cells only) wells. (C) Relative expression of hdh mRNA in primary cortical neurons after organic solvent-free, detergent-free TCV-mediated siRNA selected cargo transfection into neurons. siRNA and TCV targeting hdh are produced using the same set of ionizable cationic lipids presented in 1 (A). (D) Cell viability measured by MTT reduction method of equivalent transfection groups in primary cortical neurons using organic solvent-free, detergent-free TCVs to deliver off-target (luciferase) siRNAs. For HEK-Luc cells, N = 4 for each condition, and N = 3 wells for each condition for primary neurons. Data represent mean ± SEM. *p<0.05, **p<0.01, ***p<0.001 compared to control (cells only) condition after one-way ANOVA for each condition with Bonforroni post hoc analysis.

[0033] Figure 2 A-2D shows that the efficacy of organic solvent-free, detergent-free TCVs does not depend on the mixing method used to generate empty TCVs. (A) Relative luciferase expression in HEK-Luc cells after transfection with TCVs composed of 50% ionizable lipids and formed by T-junction mixing (DODMA-50%) or extrusion (DODMA-50%-X). (B) Cell viability from the same transfection group presented in (A) as a percentage of control (cells only) wells. (C) Relative expression of hdhmRNA in primary cortical neurons after organic solvent-free, detergent-free TCV-mediated transfection of siRNA targeting hdh using the same TCV group presented in 2(A). (D) Cell viability measured by MTT reduction of equivalent transfection groups using organic solvent-free, detergent-free TCVs to deliver off-target (luciferase) siRNA in primary cortical neurons. N=4 for each condition for HEK-Luc cells and N=3 wells for each condition for primary neurons. Data represent mean ± SEM. *p<0.05, **p<0.01, ***p<0.001 compared to control (cells only) condition after one-way ANOVA for each condition with Bonforroni post hoc analysis.

[0034] Figure 3A-3D show that organic solvent-free, detergent-free empty TCVs containing reduced amounts of ionizable lipids promote efficient siRNA delivery with reduced toxicity. (A) Relative luciferase expression in HEK-Luc cells after transfection with TCVs composed of 20% or 50% of the ionizable lipid 1,2-dioleyloxy-3-dimethylamino-propane (DODMA). (B) Cell viability from the same transfection groups presented in (A) as a percentage of control (cells only) wells. (C) Relative expression of hdh mRNA in primary cortical neurons after organic solvent-free, detergent-free TCV-mediated transfection of siRNA targeting hdh using the same TCV groups presented in 3(A). (D) Cell viability measured by MTT reduction of equivalent transfection groups in primary cortical neurons using organic solvent-free, detergent-free TCVs to deliver off-target (luciferase) siRNAs. For HEK-Luc cells, N=4 per condition, for primary neurons, N=3 wells per condition. Data represent mean ± SEM. *p<0.05, **p<0.01, ***p<0.001 after one-way ANOVA for each condition compared to control (cells only) condition, with Bonforroni post hoc analysis.

[0035] Figure 4 A, 4B show that incorporation of DOPE into an empty TCV without organic solvent and detergent does not change the TCV morphology. Cryo-TEM analysis was performed on (A) 20 / 30 / 10 / 39 / 1 mol% DODMA / DOPE / DSPC / Chol / PEG-lipid (DOPE = 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine); DSPC = 1,2-distearoyl-sn-glycero-3-phosphocholine; PEG = polyethylene glycol) and (B) DODMA / DSPC / Chol / PEG-lipid (50 / 10 / 39 / 1 mol%) TCVs. Scale bar = 100 nm.

[0036] Figure 5It is shown that the organic solvent-free, detergent-free empty TCV of this article can be used to deliver functional ribonucleoprotein (RNP). HEK293 cells are transfected with Cas9 RNP and single-stranded oligodeoxynucleotide (ssODN) repair templates, both of which are delivered by organic solvent-free, detergent-free TCV produced according to the method described herein. Cas9 protein is compounded with the guidance of the targeted GRN gene. DNA is extracted from cells 48 hours after transfection. PCR is used to specifically detect wild-type (WT) GRN alleles or mutant GRN alleles that only exist when homology-mediated repair (HDR) incorporates the delivered ssODN into the DNA double-strand breaks produced by Cas9. Mutant GRN alleles can be detected after TCV-mediated Cas9 RMP delivery, but are not present in control (Ctrl) cells.

[0037] Figure 6 Micrographs of Cas9 located in primary neurons are shown. As discussed herein, RNPs delivered via organic solvent-free, detergent-free TCVs can be detected using fluorescent antibodies against Cas9 proteins, shown in red. Untreated controls have no such red fluorescent signal. Blue signal = nucleic acid (DAPI staining), green signal = phalloidin (F-actin staining).

[0038] Figure 7 Transcriptional knockdown graphs of RNPs delivered via bench-top loading of RNPs into empty organic solvent-free, detergent-free TCVs in HEK cells are shown. HEK293 cells were transfected with Cas9 RNPs targeting luciferase. TCVs of bench-top loading (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)). When measured by qPCR, the relative levels of luciferase mRNA in HEK cells showed significant knockdown compared to the control ("control" in the figure). N = 3 per group. Data represent mean ± SEM. p = 0.0018 by Student's t-test.

[0039] Figure 8 Shown is a protein knockdown graph of RNPs delivered via bench-top loading of RNPs into empty organic solvent-free, detergent-free TCVs in HEK cells. HEK293 cells were transfected with Cas9 RNPs targeting luciferase. TCVs loaded with bench-top (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)). When measured by ONE-Glo, the relative level of luciferase protein in HEK cells showed significant knockdown compared to the control ("control" in the figure). N = 3 per group. Data represent mean ± SEM. p = 0.0003 by Student's t-test.

[0040] Fig. 9 Transcriptional knockdown diagrams of RNPs delivered via bench-top loading of RNPs into empty organic solvent-free, detergent-free TCVs in primary cortical neurons are shown. Primary cortical neurons were transfected with Cas9 RNPs targeting human huntingtin (HTT). TCVs of bench-top loading (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)). When measured by qPCR, the relative levels of HTT mRNA in primary neurons showed significant knockdown compared to the control ("gLuc" in the figure). N = 3 per group. Data represent mean ± SEM. p = 0.0039 by Student's t-test.

[0041] Fig.10 The mRNA expression diagram of mRNA delivered via organic solvent-free, detergent-free TCV in HEK cells is shown. Luciferase mRNA was delivered to HEK cells at different ratios (low = 0.029 mg mRNA / μmol lipid, medium = 0.058 mg mRNA / μmol lipid, high = 0.116 mg mRNA / μmol lipid) via organic solvent-free, detergent-free TCV (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)). Compared with the control, all ratios showed significant expression, and the lowest ratio showed the highest expression. mRNA expression was measured by ONE-Glo+Tox kit (Promega), N=3 for each condition.

[0042] Fig.11 The mRNA expression graph of mRNA delivered via organic solvent-free, detergent-free TCV in primary cortical neurons is shown. Luciferase mRNA was delivered to primary cortical neurons at different doses via organic solvent-free, detergent-free TCV (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)). All doses showed significant expression compared to the control. mRNA expression was measured by ONE-Glo+Tox kit (Promega), N=3 for each condition.

[0043] Fig.12Cell viability graphs of RNPs in organic solvent-free, detergent-free TCVs in HEK cells are shown. Cytotoxicity was assessed by delivering RNPs to HEK cells via organic solvent-free, detergent-free TCVs (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)) or using RNAiMax ("Rmax" in the figure; ThermoFisher Scientific). Organic solvent-free, detergent-free TCVs were significantly less toxic than RNAiMax, p=0.0002. Toxicity was assessed using the ONE-Glo+Tox kit (Promega), N=3 per group.

[0044] Fig.13 Photomicrographs of cell viability in primary neurons of siRNA loaded into empty organic solvent-free, detergent-free TCVs are shown. Cytotoxicity was assessed by delivery of siRNA into primary neurons via organic solvent-free, detergent-free TCVs (DODMA / DOPE / DSPC / Chol / PEG-lipids (20 / 30 / 10 / 39 / 1)) or using the commercially available Mirus TKO system (Mirus Bio). As shown in the photomicrographs, siRNA delivered via benchtop loading into empty organic solvent-free, detergent-free TCVs was significantly less toxic than the Mirus TKO system.

[0045] Fig.14 Shown is a knockdown graph of organic solvent-free, detergent-free TCV in HEK cells. siRNA was delivered via organic solvent-free, detergent-free TCV at 50% ("D-50%", prepared by T-junction mixing), 50% ("D-50% Ex", prepared by extrusion) DODMA levels and via the commercially available Mirus TKO system (Mirus Bio). The current 50% DODMA formulation showed approximately 50% knockdown, however, the Mirus TKO system performed worse. DETAILED DESCRIPTION OF THE INVENTION

[0046] Systems, compositions, devices, methods, etc. described herein provide lipid-based vesicles, generally referred to herein as transfection-active vesicles (TCVs), which are configured to safely and effectively deliver DNA and other nucleic acid-type selected cargoes into target cells. One and both of safety and efficiency are partially achieved by eliminating destabilizing agents (e.g., organic solvents (e.g., ethanol) and detergents (e.g., sodium dodecyl sulfate)) from the TCV loading and storage process (i.e., inserting the selected cargo into the TCV) and / or the TCV delivery process. The TCV delivery process may include transfecting mammalian cells (e.g., primary cells) with the selected cargo. The selected cargo may also include nucleic acids complexed with proteins, such as ribonucleoproteins (RNPs).

[0047] In some embodiments, the systems, compositions, devices, methods, etc. described herein provide empty lipid-based TCVs that are free of organic solvents and free of detergents. Loaded TCVs can be formed using gentle mixing (e.g., repeated manual reciprocating motion of the TCV-generating fluid in a pipette), SHM, T-junction mixing or extrusion methods, or other TCV mixing methods as desired.

[0048] In one aspect, the lipid-based TCV is composed of a mixture of ionizable cationic lipids, phospholipids, cholesterol, and PEG-lipids, and the composition comprising the TCV is free of organic solvents and / or detergents.

[0049] Organic solvent-free, detergent-free TCVs as discussed herein can be used to treat suitable diseases and conditions, such as by gene therapy. Organic solvent-free, detergent-free TCVs as discussed herein improve the delivery of RNA, DNA and RNP gene therapy products to human patients. Organic solvent-free, detergent-free TCVs effectively deliver gene therapy (including but not limited to mRNA, siRNA and RNP) products to brain cells or other target cells. The root cause of many human diseases is the loss of function of the desired protein or the toxic function gain of the mutant protein. Using the organic solvent-free, detergent-free TCVs herein, these problems are all treatable and even reversible.

[0050] Some examples of such treatments include gene therapy of the central nervous system for the treatment of neurological disorders (some cases of Alzheimer's disease, Parkinson's disease, Huntington's disease, frontotemporal dementia, amyotrophic lateral sclerosis, spinal muscular atrophy, etc.).

[0051] Organic solvent-free, detergent-free TCVs as discussed herein can also be used to genetically "knock down" mutant genes / gene products, for example, by targeted safe delivery of siRNA or RNPs, gene replacement therapy with mRNA, or correction of causal natural DNA mutations with RNP-mediated gene editing. Two specific examples of human diseases that can be targeted in this manner are Huntington's disease (HD) and frontotemporal dementia (FTD).

[0052] Huntington's disease is a progressive, incurable neurodegenerative disease with a dominant inheritance pattern. Expanded CAG nucleotide repeats in the Huntington (HTT) gene are responsible for the disease. The Huntingtin protein (HTT) encoded by the mutant HTT gene contains expanded polyglutamine repeats that confer toxic functional gain to the gene product. Reducing brain levels of mutant Huntington protein is currently the main therapeutic strategy being pursued to slow or prevent HD disease progression, and can be achieved and improved using the organic solvent-free, detergent-free TCVs discussed herein. TCVs loaded with siRNA targeting HTT expression or with RNP selected cargo designed to reduce Huntington protein expression or toxicity will be an effective therapy for HD. There are many causes of frontotemporal dementia, but the loss of the protein progranulin (potential brain survival factor) is a well-described cause. The organic solvent-free, detergent-free TCV discussed herein can deliver progranulin mRNA or RNP (respectively) designed to express progranulin or correct the underlying DNA mutation that causes progranulin loss, which will increase brain levels of progranulin and will be an effective therapy for FTD. Increasing progranulin with TCV expressing progranulin mRNA can also be a neuroprotective strategy for many common neurological diseases (e.g., Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis). Examples of Materials and Methods Material

[0053] 1,2-Dioleyloxy-3-dimethylamino-propane (DODMA) was purchased from Cayman Chemical (Ann Arbor, MI). 1,2-Dioleoyl-3-dimethylammonium-propane (DODAP), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), and 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) were purchased from Avanti Polar Lipids (Alabaster, AL). Cholesterol was purchased from Sigma Aldrich (St. Louis, MO). PEG-DMG was synthesized as previously described (Akinc, Zumbuehl et al., 2008). All lipids were stored as ethanol stocks. siRNA targeting firefly luciferase (siLuc) (Basha, Ordobadi et al., 2016) was purchased from Integrated DNA Technologies (Coralville, IA). siRNA targeting mouse hdh was purchased from Ambion ( Select Pre-designed siRNA, Invitrogen, Carlsbad, CA). Preparation of transfection-competent vesicles (TCVs)

[0054] The lipid components (ionizable cationic lipids, phospholipids, cholesterol and PEG-lipids) were dissolved in ethanol in appropriate proportions to achieve a final concentration of 20-35 mM total lipids. An aqueous phase containing 25 mM sodium acetate pH 4 buffer was prepared. The two solutions were combined using two established nanoparticle preparation techniques: rapid mixing and extrusion. Quick Mixing:

[0055] The organic phase containing lipids was mixed with the aqueous phase at a final flow rate of 20 mL / min and an organic:aqueous phase (v / v) ratio of 1:3 through a T-junction mixer manufactured to meet PEEK Low Pressure Tee Assembly specifications (1 / 16", 0.02 through hole, part #P-712) (Jeffs, Palmer et al., 2005; Kulkarni, Tam et al., 2017; Kulkarni, Darjuan et al., 2018). The resulting suspension was dialyzed against 1000 volumes of 25 mM sodium acetate pH 4 buffer to remove ethanol. Extrusion:

[0056] The lipids were dissolved in ethanol to a final concentration of 35 mM. Particles were formed by rapidly adding 25 mM sodium acetate pH 4 to an ethanol solution to a final concentration of 30% ethanol (v / v) as described elsewhere (Maurer, Wong et al., 2001). The resulting nanoparticle suspension was extruded three times through a 2×80 nm polycarbonate membrane at ambient temperature. After extrusion, the particles were buffer exchanged to remove ethanol. Analysis of transfected activated vesicles (TCVs)

[0057] Lipid concentration was determined by measuring cholesterol content using the T-cholesterol assay kit (Wako Chemicals, Mountain View, CA) and extrapolating total lipid concentration as described elsewhere (Chen, Tam et al., 2014). Nucleic acid encapsulation was determined using the RiboGreen assay as previously described (Chen, Tam et al., 2014; Leung, Tam et al., 2015). Cryogenic transmission electron microscopy

[0058] Cryo-TEM was performed as previously described (Kulkarni, Darjuan et al., 2018). In brief, TCV was concentrated to a total lipid concentration of approximately 20 mg / mL using an Amicon centrifugal concentration unit (10 kDa NWCO). A small amount (3-5 uL) of material was applied to a glow-discharged copper grid and rapidly frozen using a FEI Mark IV Vitrobot (Hillsboro, OR). The grid was stored in liquid nitrogen until imaging. All imaging was performed using a FEI Tecnai G2 instrument operating at 200 kV in low-dose mode. Images were captured using a FEI Eagle 4k CCD bottom-mounted detector. All sample preparation and imaging were performed at the UBC BioImaging Facility (Vancouver, BC). Cell culture and reagents:

[0059] All basal cell culture media and B27 neuronal supplement were purchased from Gibco (Thermo Fisher, Waltham, MA). Hank's balanced salt solution (HBSS), penicillin-streptomycin, L-glutamine, and trypsin solution were obtained from Hyclone (Logan, UT). HEK293 cells were seeded on clear bottom white-walled plates from Corning (Corning, NY). Primary cortical cells were seeded on tissue culture treated plates (Fisher) coated with poly-D-lysine (Sigma, St. Louis, MO). Hygromycin B was obtained from Invitrogen (Carlsbad, CA). Recombinant ApoE4 was obtained from Peprotech (Rocky Hill, NJ).

[0060] To measure cell viability and luciferase levels in HEK293 cells, the ONE-Glo+Tox kit from Promega (Madison, WI) was used. Cell viability in primary neurons was measured by the MTT in vitro toxicology kit from Sigma (St. Louis, MO). Luciferase reporter gene in HEK293 cells:

[0061] The generation of HEK293 cell lines (HEK-Luc cells) with stably integrated luciferase reporter gene constructs has been described previously (De Souza, Islam et al., 2016). Cells were maintained in DMEM high glucose supplemented with 10% fetal bovine serum, 2mM L-glutamine and 125μg / mL hygromycin B at 37°C, 95% air, 5% CO2 humidified atmosphere. Cells were seeded in white wall 96-well plates at a density of 12,000-20,000 cells / well. Primary cell culture:

[0062] Cortical cultures were prepared from embryonic day E17.5 C57BL / 6J and FVB.YAC128 mice. Briefly, cortices were dissected in ice-cold HBSS and the tissue was digested using 0.05% trypsin (Hyclone) solution at 37°C for 10 min. The cortex was then triturated 5 times by a 5 mL pipette and an additional 5-7 times of trituration with a 200 μL pipette tip. Cells were pelleted by centrifugation at 800 rpm for 5 min, washed with HBSS, and then resuspended in warm neurobasal medium supplemented with B27, 2 mM L-glutamine (Hyclone), and 1% penicillin / streptomycin (Hyclone). Cortical neuronal cultures were plated at 1.5 × 10 5 The cells were seeded at a density of 10 cells / well onto poly-D-lysine coated 24-well plates. The cells were maintained at 37°C in a humidified atmosphere of 95% air and 5% CO2. Transfection:

[0063] All reagents were mixed on the bench. Empty TCVs containing 50% cationic lipid were mixed with siRNA at a ratio of 0.058 mg siRNA / micromole lipid. TCVs containing 20% ​​cationic lipid were mixed at a ratio of 0.022 mg siRNA / micromole lipid. The TCV suspension was briefly mixed with siRNA by pipetting and incubated at room temperature for 10 minutes.

[0064] HEK293 cells were plated 24 hours before transfection. Complete DMEM medium was added to the TCV:siRNA mixture to a final concentration of 3.3 μg / mL siRNA, and a full medium change was performed during transfection.

[0065] Primary neurons were grown in vitro for 7 days before transfection. Complete neurobasal medium containing 2-6 μg / mL recombinant ApoE4 was added to the TCV:siRNA suspension and half of the medium was replaced in each well. Luciferase assay:

[0066] 48 to 72 hours after transfection, the cell viability and luminescence of HEK293 cells were determined using ONE-Glo+Tox kit (Promega) according to the manufacturer's instructions. In short, live cell reagent was added to each well, and the cells were incubated at 37°C for 30 minutes. The plate was determined under 400nm excitation on a microplate reader (POLARstar Omega microplate reader, BMG LABTECH), and read at an emission wavelength of 510nm. Then ONE-Glo reagent was added, and the plate was incubated at room temperature for 3 minutes. Luminescence was measured by the light output of the lens of the same microplate reader. Numerical values ​​are expressed as % control, and represent N=4 holes for each condition. MTT assay:

[0067] Cell viability of primary cortical neurons was determined by MTT assay 72 hours after transfection in 24-well plates. MTT reagent (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, or MTT) was reconstituted in HBSS to a final concentration of 5 mg / mL and added to each well at 10% v / v. Cells were incubated at 37°C for 4 hours. The culture medium was removed and 250 μL of solubilization solution was added to each well. The absorbance was measured at 570 nm. Values ​​are expressed as % control and represent N=3 wells per condition. Quantitative RT-PCR

[0068] The attached primary cortical cells were washed once in sterile PBS, then scraped from the plate in 600 μL lysis buffer containing 1% 2-mercaptoethanol and immediately frozen at -80 ° C. Total RNA was subsequently extracted using PureLink RNA mini kit (Invitrogen) according to the manufacturer's instructions. Reverse transcription of all samples was performed using SuperscriptVILO kit (Invitrogen) according to the manufacturer's instructions, using 250 ηg total RNA as input for cDNA synthesis, and using 5 ηg diluted RNA for quantitative PCR reaction. The quantification of hdh mRNA levels was completed using the standard curve method, wherein target mRNA and control genes were amplified in separate wells, performed using FastSybr (Applied Biosystems) and implemented on Step-One ABI system (Applied Biosystems). Each sample was run in duplicate. The relative amount of mRNA in each well was calculated as the ratio between hdh mRNA and control gene Csnk2a2. Numerical values ​​are expressed as % control and represent each condition N=3 wells. Ribonucleoprotein (RNP) composites and formulations All materials used for RNP preparation, including guide RNA (gRNA), tracrRNA, single-stranded oligodeoxynucleotide (ssODN), and recombinant Cas9 protein, were obtained from IDT (San Jose, CA). IDT (San Jose, CA) provided the gRNA sequence for targeting luciferase. The gRNA sequence targeting human progranulin (GRN) binds to exon 5 of the gene. The ssODN sequence for homology-mediated repair (HDR) was engineered to introduce a 4 bp deletion into exon 5 of GRN.

[0069] RNP assembly was performed according to the manufacturer's instructions. In short, a guide RNA (gRNA) complex was formed by incubating an equimolar ratio of crRNA:tracrRNA (e.g., 1 μM tracrRNA and 1 μM gRNA) at 95 ° C for 5 minutes. The mixture was then cooled at room temperature for 20-30 minutes. RNPs were subsequently formed by mixing gRNA duplexes with Cas9 proteins in an equimolar ratio and allowing the mixture to stand at room temperature for 5 minutes before use. Transfection of mammalian cells with nucleic acids:

[0070] Empty organic solvent-free, detergent-free TCVs discussed herein and commercially available reagents for comparison were mixed with the selected cargo on the bench. TCVs were mixed with nucleic acid-based selected cargos at various ratios of 0.01-0.2 mg nucleic acid per micromole lipid. The TCV suspension was briefly mixed with siRNA by pipetting and incubated at room temperature for 10 minutes.

[0071] HEK293 cells were plated 24 hours prior to transfection. Complete DMEM medium was added to the TCV:nucleic acid mixture to a final concentration of 0.33-3.3 μg / mL siRNA or 0.1-1 μg / mL mRNA, and a full medium change was performed at the time of transfection. Primary neuronal cells were grown in vitro for 7 days prior to transfection. Complete neurobasal medium containing 2-6 μg / mL recombinant ApoE4 was added to the TCV:nucleic acid suspension, and half of the medium was changed in each well.

[0072] Treat cells with Mirus TransIT-TKO following the manufacturer's instructions. Briefly, add Mirus TransIT-TKO to serum-free medium at a concentration of 5 μl Mirus / 100 μL serum-free medium. Then add siRNA to the tube, mix gently with a pipette, and incubate at room temperature for 15-30 minutes. Then transfer the solution to the cells, with a final concentration of 5 μL Mirus / 1 mL complete medium. The final concentration of siRNA is 25 nM. Transfection of mammalian cells with RNPs:

[0073] 0.5-20 mM TCV and 0.5-20 μM RNP were combined at a molar ratio of 467-5000 and incubated at room temperature for 10 minutes. A 1-10 μM ssODN solution was combined with TCV alone and the mixture was incubated at room temperature for 5-15 minutes. In some cases, an equimolar amount of ssODN was added to the RNP complex solution before adding TCV.

[0074] Combine the TCV and ssODN mixture containing RNPs and add complete medium to a final concentration of 10-200 nM RNPs and ssODNs each. Perform a full medium change on HEK cells plated 24 hours earlier. Grow primary neuronal cells in vitro for 5-7 days prior to transfection. Add complete neurobasal medium containing 2-6 μg / mL recombinant ApoE4 to the TCV:RNP mixture and replace half of the medium in each well.

[0075] Cells were treated with Lipofectamine RNAiMAX reagent following the manufacturer's instructions. Briefly, RNP complexes were prepared and added to a mixture of serum-free medium and RNAiMAX, incubated at room temperature for 5 min, and added to plated cells. PCR detection of homology-mediated repair Polymerase chain reaction (PCR) was performed using forward primers specific for wild-type (WT) or mutant GRN alleles and universal reverse primers to amplify GRN exon 5 from genomic DNA extracted from transfected HEK293 cultures. PCR was performed using MyTaq (Bioline, USA) according to the manufacturer's instructions. PCR products were separated by gel electrophoresis on 1.5% agarose gels stained with SybrSafe and imaged under UV light. Immunocytochemistry

[0076] The cells were fixed for 15 minutes using a 3-4% paraformaldehyde solution. The cells were permeabilized in PBS (PBST) containing 0.1% Triton-X for 15 minutes. The cells were incubated overnight at 4 ° C with PBST containing a 1:1000 anti-Cas9 (Invitrogen) antibody mixture. The cells were washed three times with PBS and incubated at room temperature for 1 hour with a 1:1000 mixture of Alexa Fluor 594 fluorescent secondary antibody (Invitrogen) and phalloidin-iFluor 488CytoPainter antibody (Abcam), washed again and incubated with a solution containing DAPI for 5 minutes to visualize the nucleus. statistics

[0077] All statistical comparisons were performed with one-way analysis of variance (ANOVA) with Bonferroni post hoc analysis to compare individual means with control treated cells and corrected for multiple comparisons (Prism 6, Graphpad Software Inc.). In the case of only two groups, Student's t-test was used to compare individual means. P-values ​​less than 0.05 were considered significant. Results related examples Example 1: Empty transfection-competent vesicles (TCVs) effectively encapsulate nucleic acids in the absence of organic solvents

[0078] Empty TCV preparations produced by T-junction or SHM mixing showed encapsulation efficiencies of approximately 85% or more. We first tested the ability of TCVs composed of ionizable cationic lipids to encapsulate nucleic acids without the aid of organic solvents or detergents, spanning the range of observed in vivo gene silencing efficacy (DODMA>>DLinDAP>DODAP) ("DLinDAP" is 1,2-dilineoyl-3-dimethylammonium-propane). Notably, in the absence of either, a preparation composed of ionizable lipids / DSPC / Chol / PEG-lipids (50 / 10 / 39 / 1 mol%) achieved almost complete siRNA encapsulation (>85%) after mixing at a ratio of 0.058 mg siRNA / micromole lipid at pH 4 and subsequent neutralization with PBS (Table 1). The assay to determine encapsulation is based on the exclusion of RNA-binding dyes from nucleic acids by lipid components. Therefore, encapsulation is considered to be the sequestration of RNA from the external culture medium in an ultra-instantaneous manner (i.e., stable encapsulation). Despite the lack of organic solvents or detergents in the production process, the obtained TCV formulations surprisingly showed similar encapsulation efficiency as LNP-siRNA generated by rapid mixing techniques using organic solvents reported elsewhere (Belliveau, Huft et al., 2012; Chen, Tam et al., 2014; Leung, Tam et al., 2015; Chen, Tam et al., 2016). Table 1: Nucleic acid encapsulation efficiency of different TCV formulations. Example 2: siRNA in organic solvent-free, detergent-free empty TCVs shows robust knockdown in immortalized cells and primary neurons

[0079] The ability to encapsulate nucleic acids and subsequently deliver them in a nontoxic manner represents two separate hurdles. Having established that the organic solvent-free / detergent-free lipid-based TCVs discussed above effectively encapsulate nucleic acids, their ability to silence genes and their effects on cell viability were tested in two contexts, Figure 1 A-1D. First, an organic solvent-free, detergent-free empty TCV was mixed with siLuc using benchtop loading and used to treat HEK-Luc cells. Surprisingly, the DODMA-based TCV showed about 50% knockdown, performing better than DLinDAP and DODAP, which showed no signs of knockdown ( Figure 1 A). All formulations showed no toxicity as measured by cell viability compared to untreated cells ( Figure 1 B). Secondly, the efficacy and toxicity of TCV-delivered siRNA were tested against the hdh gene in primary mouse cortical neurons. DODMA-TCV was again ( Figure 1 C) shows approximately 50% gene knockdown efficacy, while DLinDAP TCV shows lower knockdown and DODAP-TCV is indistinguishable from untreated cells. It should be noted that primary neurons are highly susceptible to toxic effects of harmful transfection reagents such as those currently commercially available. Fig.13 The differences in impact on vitality are highlighted. Example 3: Multiple hybrid methods can produce effective organic solvent-free, detergent-free empty TCV

[0080] In order to determine the role of mixing in the preparation process and to achieve Figure 1 Organic solvent-free, detergent-free lipid-based empty TCVs containing ionizable lipids (e.g., DODMA) were prepared by two methods, T-junction mixing and extrusion, with the resulting particle size of the indicated efficacy. Figure 2 A shows that after bench-top loading of siRNA into empty TCVs, luciferase was significantly knocked down in HEK-Luc cells using both methods. There were no significant differences in viability between cells treated with particles generated by T-junction or extrusion ( Figure 2 B). Next, primary cortical neurons were treated with the same solvent-free, detergent-free, lipid-based TCV preparation and it was determined that the particles generated by both methods had similar potency ( Figure 2 C) and similar cell viability ( Figure 2 D). In contrast, the toxicity of existing transfection methods in primary cultures ( Fig.13 ) deviates from the goal of a non-toxic but effective formulation. Example 4: Organic solvent-free, detergent-free empty TCVs containing reduced amounts of ionizable lipids promote efficient siRNA delivery with reduced toxicity

[0081] The established lipid compositions currently used in clinical formulations (see Patisiran) include a large amount of ionizable cationic lipids (50 mol%) (Jayaraman, Ansell et al., 2012; Suhr, Coelho et al., 2015). However, such high amounts can improve the effective dose (ED) to achieve 50% gene silencing in vivo. 50 )(Jayaraman, Ansell et al., 2012), but the persistence of lipid metabolites after administration (Maier, Jayaraman et al., 2013; Sabnis, Kumarasinghe et al., 2018) and the toxicity associated with these molecules make the formulation toxic in high-dose regimens and repeated administrations (or to sensitive cell types). Current compositions, TCVs, etc. can be composed of materials that are biodegradable or promote elimination. Therefore, current compositions, TCVs, etc. reduce the amount of toxic components that maintain transfection efficacy.

[0082] The ability of a formulation consisting of DODMA / DOPE / DSPC / Chol / PEG-lipid (20 / 30 / 10 / 39 / 1 mol %, respectively) to silence luciferase transfection in HEK-Luc cells was tested. A 40% knockdown of luciferase expression ( Figure 3 A) without significant toxicity ( Figure 3 B). Next, we tested the ability of TCVs containing 20 mol% ionizable lipids to deliver siRNA to primary neurons compared to DODMA-TCVs containing 50 mol% ionizable lipids. All formulations showed ~60% knockdown of hdh ( Figure 3 C), while the DODMA preparation produced by T-junction mixing showed significantly improved cell viability ( Figure 3 C). Example 5: Incorporation of DOPE does not change the morphology of empty TCVs without organic solvents or detergents

[0083] Improving H in nucleic acid delivery vectors II The potential for phase formation may be an important factor in promoting membrane fusion in endosomes (Hafez, Maurer et al., 2001). II Two exemplary lipids for the phase are DOPE (alone) and DODMA (when protonated and bound to anionic lipids). To determine whether incorporation of DOPE into organic solvent-free, detergent-free TCVs would result in premature formation of H II Phase, cryo-TEM was performed on 20 mol % DODMA-TCV and the same preparation consisting of 50 mol % DODMA. The obtained structure ( Figure 4 A, 4B) Visualized as a double-layer structure without H IISigns of phase.

[0084] Previous work by others has shown that H is present in core LNP formulations regardless of siRNA content. II -similar internal structure (Leung, Hafez et al., 2012; Leung, Tam et al., 2015). Although it has been shown that LNP-siRNA does not contain such a structure, but rather fixes siRNA between closely packed lipid layers (Kulkarni, Darjuan et al., 2018), so that the entire particle presents a multilayer or onion-like morphology. In the absence of siRNA, the LNP formulation adopts an electron-dense core containing oil-phase lipids. Therefore, the examples herein demonstrate that the TCV morphology is significantly different from the LNP system, but still has a high transfection efficacy. Example 6: Organic solvent-free, detergent-free empty TCVs can be used to deliver functional ribonucleoproteins (RNPs).

[0085] like Figure 5 As shown, empty organic solvent-free, detergent-free TCVs were also tested herein for their ability to deliver proteinaceous cargo of choice complexed with nucleic acids into mammalian cells. Briefly, ribonucleoprotein complexes consisting of recombinant Cas9 protein and guide RNA targeting exon 5 of the progranulin gene were assembled and combined with empty TCVs loaded by benchtop loading (DODMA / DOPE / DSPC / Chol / (20 / 30 / 10 / 40 mol %, respectively) at a molar ratio of 467:1. In addition, a single-stranded oligonucleotide designed to introduce a 4 bp deletion in exon 5 of the progranulin gene was mixed with the TCV at a molar ratio of 4275:1 (TCV:nucleic acid). The two TCV preparations containing the respective selected cargos were combined to reach a final concentration of 10 nM RNP and 10 nM ssODN, which were then added to HEK cells. After 48 h, PCR was performed to determine whether homology-directed repair of the progranulin gene target site had occurred using wild-type or mutant allele-specific forward primers. Figure 5 As shown, exposure of cells to a combination of TCVs containing each of the ribonucleoprotein complex and ssODN resulted in the insertion of a 4 bp deletion ( Figure 5 The second lane of the PCR reaction was labeled as mutant), while the untreated control cells did not result in any genetic changes in exon 5 of the progranulin gene ( Figure 5 3rd and 4th lanes). Example 7: Further examples of organic solvent-free, detergent-free empty TCVs for delivery of functional ribonucleoproteins (RNPs).

[0086] Using the methods discussed above, empty organic solvent-free, detergent-free TCVs were used to deliver functional ribonucleoproteins (RNPs).

[0087] Figure 6 Micrographs of Cas9 located in primary neurons are provided. As discussed herein, RNPs delivered by organic solvent-free, detergent-free TCVs can be observed as fluorescent signals in primary neurons; untreated controls have no such fluorescent signals. More specifically, immunocytochemistry of primary neuronal cells shows that Cas9 protein (red) is localized in the nuclei (blue) of cortical neurons derived from mice. Cells are also stained with phalloidin (green) to show cell morphology.

[0088] Figure 7 Provided is a graph showing gene knockdown in HEK cells by RNPs delivered via organic solvent-free, detergent-free TCV. RNPs delivered into HEK cells via organic solvent-free, detergent-free TCV showed significant knockdown of luciferase transcripts compared to controls ("control" in the graph). Figure 8 A graph showing protein knockdown in HEK cells by RNPs delivered via organic solvent-free, detergent-free TCV is provided. RNPs delivered into HEK cells via organic solvent-free, detergent-free TCV showed significant knockdown of luciferase protein compared to the control ("Control" in the graph), p=0.0003.

[0089] Fig. 9 A graph is provided showing that RNPs delivered via organic solvent-free, detergent-free TCV show gene knockdown in primary neurons. RNPs delivered via organic solvent-free, detergent-free TCV to primary cortical neurons show significant mRNA knockdown as determined by quantitative real-time PCR (qRT-PCR), p=0.0039.

[0090] Turning to some further discussion of these figures, Figure 7 and Figure 8 The RNPs delivered by the empty TCVs of the bench-top loading paper showed a strong knockdown of the reporter gene luciferase in HEK cells. This was confirmed by measuring the luciferase production (functional protein) and the mRNA levels of luciferase mRNA measured by qRT-PCR. The same RNP delivery method was also used to disrupt the expression of the huntingtin gene in cortical neurons derived from FVB.YAC128 mice ( Fig. 9 ), which expresses the full-length human Huntington's gene carrying the disease mutation. After incubation with the TCV:RNP mixture for 72 hours, qRT-PCR was used to quantify the mRNA levels of the Huntington's gene in primary cortical neurons. Example 8: Example of mRNA delivery via organic solvent-free, detergent-free TCV

[0091] Using the methods discussed above, bench-top loading of organic solvent-free, detergent-free empty TCVs was used to deliver mRNA.

[0092] Fig.10 Provided is a graph showing the expression of mRNA delivered via organic solvent-free, detergent-free TCV in HEK cells. mRNA was delivered to HEK cells at different ratios via organic solvent-free, detergent-free TCV (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)), low = 0.029 mg mRNA / micromole lipid, medium = 0.058 mg mRNA / micromole lipid, high = 0.116 mg mRNA / micromole lipid. All ratios showed significant expression compared to the control, with the lowest ratio showing the highest expression.

[0093] Fig.11 Provided are graphs showing expression of mRNA delivered via bench-top loaded organic solvent-free, detergent-free empty TCVs in primary cortical neurons. mRNA was delivered to primary cortical neurons at different doses via organic solvent-free, detergent-free TCVs (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)). All doses showed significant expression compared to controls.

[0094] Turning to some further discussion of these figures, Fig.10 It was demonstrated that benchtop loading of organic solvent-free, detergent-free empty TCVs as discussed herein can be used to deliver mRNA encoding functional proteins into cells. Briefly, mRNA encoding firefly luciferase mRNA was gently mixed with organic solvent-free, detergent-free TCVs in a range of 0.029-0.116 mg nucleic acid:1 micromolar lipid ratio using a pipette. The mixture was incubated at room temperature for 5-20 minutes before adding complete medium and then transferred to a plate containing HEK cells (see Fig.10 ) or primary cortical neurons ( Fig.11 ) wells. Luciferase production was measured using Promega's ONE-Glo Luciferase Assay Kit according to the manufacturer's instructions. The results showed that luciferase protein was produced in these cell types over a range of selected cargo: TCV concentrations and doses. Example 9: Comparison of organic solvent-free, detergent-free TCV with commercial products

[0095] Using the methods discussed above, bench-top loaded organic solvent-free, detergent-free empty TCVs were used to deliver siRNA or RNPs into HEK cells or primary neurons and then compared to equivalent transfections using commercially available systems. The organic solvent-free, detergent-free TCVs described herein outperform commercially available systems.

[0096] Fig.12 Figures showing cell viability of organic solvent-free, detergent-free TCV in HEK cells are provided. RNPs were delivered to HEK cells via organic solvent-free, detergent-free TCV (DODMA / DOPE / DSPC / Chol (20 / 30 / 10 / 40)) or using RNAiMax ("Rmax" in the figure; ThermoFisher Scientific) for cytotoxicity assessment. Organic solvent-free, detergent-free TCV had significantly reduced toxicity compared to RNAiMax, p=0.0002.

[0097] Fig.13 Micrographs showing bench-top loading of siRNA into empty TCVs without organic solvents and detergents in primary neurons are provided. siRNA was delivered to primary neurons via TCVs without organic solvents and detergents (DODMA / DOPE / DSPC / Chol / PEG-lipids (20 / 30 / 10 / 39 / 1)) or using the commercially available Mirus TKO system (Mirus Bio) for cytotoxicity assessment. As shown in the micrographs, the toxicity of the TCVs without organic solvents and detergents was significantly reduced compared to the Mirus TKO system.

[0098] Fig.14 A graph showing knockdown of organic solvent-free, detergent-free TCV in HEK cells is provided. siRNA was delivered via organic solvent-free, detergent-free TCV at 50% ("D-50%", prepared by T-junction mixing), 50% ("D-50% Ex", prepared by extrusion) DODMA levels and via the commercially available Mirus TKO system (Mirus Bio). The current 50% DODMA formulation showed approximately 50% knockdown, while the Mirus TKO system performed significantly worse.

[0099] Turning to some further discussion of these figures, Fig.12Benchtop loading of siRNA into empty TCVs without organic solvents and detergents as discussed herein was shown to have low toxicity and effective knockdown of expression in both mouse-derived primary neuronal cells and HEK cell lines. For treatment of primary cortical neurons, TCVs were mixed with siRNA at a ratio of approximately 0.022-0.058 mg nucleic acid: 1 micromole lipid and transferred to wells containing primary neuronal cells. Fig.13 The light micrographs in the Figures, all taken at the same magnification, show that in both control and TCV-treated wells, cells remain healthy, with intact processes and very low numbers of dead cells. In Mirus TransIT-TKO-treated wells, cells appear rather unhealthy, with broken cell processes and an increased number of small, condensed (dead) cells.

[0100] for Fig.12 HEK cells were treated with Lipofectamine RNAiMAX and TCV containing RNP selected cargo. HEK cells were treated with RNP and TCV or RNAiMAX reagents at a final concentration of 5-50nM. Cell viability was assessed using the Promega ONE-Glo+Tox kit and compared to untreated control cells. HEK cultures treated with RNAiMAX showed a significant decrease in overall health compared to both control and TCV treated wells.

[0101] Fig.14 It is shown that compared with the commercially available product Mirus LT-TKO, the desktop loading of the empty TCV without organic solvent and detergent discussed herein is effective in delivering the selected goods of siRNA. TCV and siRNA targeting the luciferase gene are incubated at room temperature for 5-10 minutes at a ratio of about 0.022-0.058mg nucleic acid: 1 micromole lipid. HEK cells are treated with Mirus LT-TKO according to the manufacturer's instructions. When treated, the culture medium in the well is completely replaced with fresh growth medium containing siRNA:TCV or siRNA:Mirus LT-TKO mixture. After 72 hours of treatment, the cell viability and luciferase production of HEK cells are determined using the Promega ONE-Glo+Tox kit, and all cells are compared with untreated control wells. References Akinc, A., A. Zumbuehl et al., (2008). "A combinatorial library of lipid-likematerials for delivery of RNAi therapeutics." NatBiotechnol 26(5):561-569. Basha, G., M. Ordobadi et al., (2016). "Lipid Nanoparticle Delivery of siRNA to Osteocytes Leads to Effective Silencing of SOST and Inhibition of Sclerostin In Vivo." MolTherNucleicAcids 5(9):e363. Belliveau, N.M., J. Huft et al., (2012). "Microfluidic Synthesis of Highly Potent Limit-size Lipid Nanoparticles for In Vivo Delivery of siRNA." Mol Ther Nucleic Acids 1:e37. Chen, S., Y.Y. Tam et al., (2014). "Development of lipid nanoparticle formulations of siRNA for hepatocyte gene silencing following subcutaneous administration." JControlRelease 196:106 - 112. Chen, S., Y.Y. Tam et al., (2016). "Influence of particle Size on the in vivo potency of lipid nanoparticle formulations of siRNA." JControl Release . De Souza, R.A., S.A. Islam et al., (2016). "DNA methylation profiling in human Huntington's disease brain." Hum MolGenet 25(10):2013 - 2030. Digiacomo, L., S. Palchetti et al., (2018). "Cationic lipid / DNA complexes manufactured by microfluidics and bulk self-assembly exhibit different transfection behavior." BiochemBiophys Res Commun 503(2):508 - 512. Hafez, I.M., N. Maurer et al., (2001). "On the mechanism whereby cationic lipids promote intracellular delivery of polynucleic acids." GeneTher 8(15):1188 - 1196. Jayaraman, M., S.M. Ansell et al., (2012). "Maximizing the potency of siRNA lipid nanoparticles for hepatic gene silencing in vivo." Angew ChemIntEdEngl 51(34):8529 - 8533. Jeffs, L.B., L.R. Palmer et al., (2005). "A Scalable, Extrusion - Free Method for Efficient Liposomal Encapsulation of Plasmid DNA." Pharm-Res 22(3):362 - 372. Kulkarni, J.A., M.M. Darjuan et al., (2018). "On the Formation and Morphology of Lipid Nanoparticles Containing Ionizable Cationic Lipids and siRNA." ACSNano 12(5):4787 - 4795. Kulkarni, J.A., Y.Y.C. Tam et al., (2017). "Rapid Synthesis of Lipid Nanoparticles Containing Hydrophobic Inorganic Nanoparticles." Nanoscale . Leung, A.K., I.M. Hafez et al., (2012). "Lipid Nanoparticles Containing siRNA Synthesized by Microfluidic Mixing Exhibit an Electron-Dense Nanostructured Core." J Phys Chem C Nanomater Interfaces 116(34):18440 - 18450. Leung, A.K., Y.Y. Tam et al., (2015). "Microfluidic Mixing: A General Method for Encapsulating Macromolecules in Lipid Nanoparticle Systems." J Phys Chem B 119(28):8698 - 8706. Lin, P.J., Y.Y. Tam et al., (2013). "Influence of cationic lipid composition on uptake and intracellular processing of lipid nanoparticle formulations of siRNA." Nanomedicine 9(2):233 - 246. Maier, M.A., M. Jayaraman et al., (2013). "Biodegradable lipids enabling rapidly eliminated lipid nanoparticles for systemic delivery of RNA therapeutics." Mol Ther 21(8):1570 - 1578. Maurer, N., K.F. Wong et al., (2001). "Spontaneous entrapment of polynucleotides upon electrostatic interaction with ethanol-destabilized cationic liposomes." Biophys J 80(5):2310 - 2326. Palchetti, S., D. Pozzi et al., (2017). "Manipulation of lipoplex concentration at the cell surface boosts transfection efficiency in hard-to-transfect cells." Nanomedicine 13(2):681-691. Pardi, N., S. Tuyishime et al., (2015). "Expression kinetics of nucleoside-modified mRNA delivered in lipid nanoparticles to mice by various routes." J Control Release 217:345-351. Pozzi, D., C. Marchini et al., (2012). "Transfection efficiency boost of Cholesterol-containing lipoplexes." Biochim BiophysActa 9(43):22. Rungta, R. L., H. B. Choi et al., (2013). "Lipid Nanoparticle Delivery of siRNA to Silence Neuronal Gene Expression in the Brain." MolTherNucleicAcids 3(2):65. Sabnis, S., E. S. Kumarasinghe et al., (2018). "A Novel Amino Lipid Series for mRNA Delivery: Improved Endosomal Escape and Sustained Pharmacology and Safety in Non-human Primates." MolTher 26(6):1509-1519. Scherphof, G. and H. Morselt (1984). "On the size-dependent disintegration of small unilamellar phosphatidylcholine vesicles in rat plasma. Evidence of complete loss of vesicle structure." BiochemJ 221(2):423 - 429. Semple, S.C., A. Akinc et al., (2010). "Rational design of cationic lipids for siRNA delivery." NatBiotechnol 28(2):172 - 176. Semple, S.C., S.K. Klimuk et al., (2001). "Efficient encapsulation of antisense oligonucleotides in lipid vesicles using ionizable aminolipids: formation of novel small multilamellar vesicle structures." Biochimica etBiophysicaActa(BBA)-Biomembranes 1510(1):152 - 166. Suhr, O.B., T. Coelho et al., (2015). "Efficacy and safety of patisiran for familial amyloidotic polyneuropathy: a phase II multi-dose study." Orphanet Journal of Rare Diseases 10(1):109. Tam, P., M. Monck et al., (2000). "Stabilized plasmid-lipid particles for systemic gene therapy." GeneTherapy 7:1867. Wang, Y., L. Miao et al., (2015). "Delivery of oligonucleotides with lipid nanoparticles." AdvDrug Deliv Rev 87:68 - 80. Wheeler, JJ, L.Palmer et al., (1999). 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[0102] Unless the context or definitions clearly indicate otherwise, all terms used herein are used according to their ordinary meanings. In addition, unless otherwise expressly indicated, the use of "or" in this specification includes "and" and vice versa. Non-limiting terms should not be interpreted as limiting terms unless otherwise expressly indicated or the context clearly indicates otherwise (for example, "including", "having" and "comprising" generally mean "including but not limited to"). The singular forms included in the claims (for example, "a", "an", and "the") include plural references unless otherwise expressly indicated or the context clearly indicates otherwise.

[0103] Unless otherwise stated, adjectives such as "substantially" and "about" used herein to modify conditions or relational characteristics of one or more features of the embodiments indicate that the condition or feature is within an acceptable tolerance range for performing the embodiment for the intended application.

[0104] The scope of the apparatus, systems, methods, etc. of the present invention includes both means-plus-function and step-plus-function concepts. However, unless the word "means" is specifically recited in a claim, the claim shall not be interpreted as indicating a "means-plus-function" relationship, in which case the claim shall be interpreted as indicating a "means-plus-function" relationship. Similarly, unless the word "step" is specifically recited in a claim, the claim shall not be interpreted as indicating a "step-plus-function" relationship, in which case the claim shall be interpreted as indicating a "step-plus-function" relationship.

[0105] In summary, it should be understood that although specific embodiments have been discussed herein for illustrative purposes, various modifications may be made without departing from the spirit and scope of the discussion herein. Therefore, the systems and methods, etc. include modifications and all permutations and combinations of the subject matter described herein, and are not limited to the appended claims or other claims that have sufficient support in the discussion and drawings herein.

Claims

1. A method for encapsulating a selected cargo into a lipid-based transfection-competent vesicle (TCV), comprising: - providing a water-based solution comprising a lipid-based TCV, wherein the water-based solution does not contain a destabilizing agent; as well as - mixing the selected cargo into a solution under suitable conditions and for a sufficient time to allow the selected cargo to be encapsulated within the lipid-based TCV to provide a lipid-based TCV-encapsulated selected cargo, wherein the mixing is performed in the absence of an organic solvent or detergent.

2. The method of claim 1, wherein the destabilizing agent is at least one of an organic solvent or a detergent.

3. The method of claim 1, wherein the organic solvent is ethanol.

4. The method of claim 1, wherein the organic solvent is methanol.

5. The method of claim 1, wherein the organic solvent is isopropanol.

6. The method of claim 1, wherein the organic solvent is tetrahydrofuran (THF).

7. The method of claim 1, wherein the organic solvent is dimethyl sulfoxide (DMSO).

8. The method of claim 1, wherein the organic solvent is dimethylformamide (DMF).

9. The method of claim 1, wherein the organic solvent is acetonitrile (ACN).

10. The method of claim 1, wherein the detergent is sodium dodecyl sulfate (SDS).

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