Patent Application
20210363544
The contents of the sequence listing text file named “048831-516001WO_Sequence_Listing_ST25.txt”, which was created on Dec. 21, 2017 and is 31,000 bytes in size, is hereby incorporated by reference in its entirety.
The invention relates to the delivery of agents into mammalian cells.
Variability in cell transfection efficiency exists among different cell types. Transfection of suspension cells, e.g., non-adherent cells, has proven to be very difficult using conventional methods. Thus, a need exists for compositions and methods to facilitate transfection of such cells.
The invention provides a solution to the problem of delivering payload/cargo compounds and compositions into non-adherent cells. Accordingly, a method of delivering a payload across a plasma membrane of a non-adherent cell comprises the steps of providing a population of non-adherent cells and contacting the population of cells with a volume of an isotonic aqueous solution, the aqueous solution including the payload and an alcohol at greater than 5 percent (v/v) concentration. For example, the alcohol comprises ethanol, e.g., greater than 10% ethanol. In some examples, the aqueous solution comprises between 20-30% ethanol, e.g., 27% ethanol.
The aqueous solution for delivering cargo to cells comprises a salt, e.g., potassium chloride (KCl) in between 12.5-500 mM. For example, the solution is isotonic with respect to the cytoplasm of a mammalian cell such as a human T cell. Such an exemplary isotonic delivery solution 106 mM KCl.
The methods are used to deliver any cargo molecule or molecules to mammalian cells, adherent or non-adherent and are particularly useful to deliver cargo to non-adherent cells because of the difficulties associated with doing so prior to the invention. In some examples, the non-adherent cell comprises a peripheral blood mononuclear cell, e.g., the non-adherent cell comprises an immune cell such as a T cell (T lymphocyte). An immune cell such as a T cell is optionally activated with a ligand of CD3, CD28, or a combination thereof. For example, the ligand is an antibody or antibody fragment that binds to CD3 or CD28 or both.
The method involves delivering the cargo in the delivery solution to a population of non-adherent cells comprising a monolayer. For example, the monolayer is contacted with a spray of aqueous delivery solution. The method delivers the payload/cargo (compound or composition) into the cytoplasm of the cell and wherein the population of cells comprises a greater per cent viability compared to delivery of the payload by electroporation or nucleofection—a significant advantage of the Soluporation system.
Any compound or composition can be delivered. For example, the payload comprises a messenger ribonucleic acid (mRNA), e.g., a mRNA that encodes a gene-editing composition. For example, the gene editing composition reduces the expression of an immune checkpoint inhibitor such as PD-1 or PD-Ll. In some examples, the mRNA encodes a chimeric antigen receptor (CAR).
In certain embodiments, the monolayer of non-adherent/suspension cells resides on a membrane filter. In some embodiments, the membrane filter is vibrated following contacting the cell monolayer with a spray of the delivery solution. The membrane filter may be vibrated or agitated before, during, and/or after spraying the cells with the delivery solution.
Also within the invention is a system comprising: a housing configured to receive a plate comprising a well; a differential pressure applicator configured to apply a differential pressure to the well; a delivery solution applicator configured to deliver atomized delivery solution to the well; a stop solution applicator configured to deliver a stop solution to the well; and a culture medium applicator configured to deliver a culture medium to the well. A stop solution is one that lacks a cell membrane permeabilizing agent, e.g., ethanol. An example phosphate buffered saline or any physiologically-compatible buffer solution. The system optionally further comprises: an addressable well assembly configured to: align the differential pressure applicator adjacent the well for applying the differential pressure to the well; align the delivery solution applicator adjacent the well for delivering the atomized delivery solution to the well; align the stop solution applicator adjacent the well to deliver the stop solution to the well; and/or align the culture medium applicator adjacent the well to deliver the culture medium to the well.
The addressable well assembly can include a movable base-plate configured to receive the plate comprising the well and move the plate in at least one dimension. The addressable well assembly can include a mounting assembly configured to couple to the delivery solution applicator, the stop solution applicator and the culture medium applicator.
The delivery solution applicator can include a nebulizer. The delivery solution applicator can be configured to deliver 10-300 micro liters of the delivery solution per actuation.
The system can include a temperature control system configured to control a temperature of the delivery solution and/or of the plate comprising the well.
The system can include an enclosure configured to control an environment of the plate comprising the well.
The differential pressure applicator can include a nozzle assembly configured to faun a seal with an opening of the well and to deliver a vapor to the well to increase or decrease pressure within the well, thereby driving a liquid portion of the culture medium from the well such that a layer of cells remains within the well.
The stop solution applicator can comprise a needle emitter configured to couple to a stop solution reservoir.
The culture medium applicator can comprise a needle emitter configured to couple to a culture medium reservoir.
The system can further comprise a controller configured to: receive user input; operate the delivery solution applicator to deliver the atomized delivery solution to a cellular monolayer within the well; incubate, for a first incubation period, the cellular monolayer after application of the delivery solution; operate, in response to expiration of the first incubation period, the stop solution applicator to deliver the stop solution to the cellular monolayer; and incubate, for a second incubation period and in response to application of the stop solution, the cellular monolayer. The controller can be further configured to: iterate operation of the delivery solution applicator, incubation for the first incubation period, operation of the stop solution applicator, and incubation for the second incubation period for a predetermined number of iterations.
The system can further comprise a controller configured to: operate the positive pressure system to remove supernatant from the well to create a cellular monolayer within the well.
The delivery solution applicator can include a spray head and a collar encircling a distal end of the spray head, wherein the collar is configured to prevent contamination between wells in a multi-well plate, wherein the collar is configured to provide a gap between the plate and the collar.
The delivery solution applicator can include a spray head and a film encircling a distal end of the spray head.
The system can further comprise a vibration system coupled to a membrane holder and configured to vibrate a membrane.
The system can further comprise the plate, wherein the well is configured to contain a population of non-adherent cells.
The delivery solution includes an isotonic aqueous solution, the aqueous solution including the payload and an alcohol at greater than 5 percent (v/v) concentration. The alcohol can comprise ethanol. The aqueous solution can comprise greater than 10% ethanol. The aqueous solution can comprise between 20-30% ethanol. The aqueous solution can comprise 27% ethanol. The aqueous solution can comprise between 12.5-500 mM KCl. The aqueous solution can comprise between 106 mM KCl.
The non-adherent cells can comprise a peripheral blood mononuclear cell. The non-adherent cells can comprise an immune cell. The non-adherent cells can comprise non-adherent cell comprises a T lymphocyte. The population of non-adherent cells can comprise a monolayer.
The payload can comprise a messenger ribonucleic acid (mRNA). The mRNA can encode a gene-editing composition. For example, the gene editing composition reduces the expression of PD-1. The mRNA can encode a chimeric antigen receptor.
The system can be used to deliver a cargo compound or composition to a mammalian cell.
In another aspect, a composition comprises an isotonic aqueous solution, the aqueous solution comprising KCl at a concentration of 10-500 mM and ethanol at greater than 5 percent (v/v) concentration for use to deliver a cargo compound or composition to a mammalian cell. The KCl concentration can be 106 mM and said alcohol concentration can be 27%.
The compounds that are loaded into the MPS composition are processed or purified. For example, polynucleotides, polypeptides, or other agents are purified and/or isolated. Specifically, as used herein, an “isolated” or “purified” nucleic acid molecule, polynucleotide, polypeptidc, or protein, is substantially free of other cellular material, or culture medium when produced by recombinant techniques, or chemical precursors or other chemicals when chemically synthesized. Purified compounds are at least 60% by weight (dry weight) the compound of interest. Preferably, the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight the compound of interest. For example, a purified compound is one that is at least 90%, 91%, 92%, 93%, 94%, 95%, 98%, 99%, or 100% (w/w) of the desired compound by weight. Purity is measured by any appropriate standard method, for example, by column chromatography, thin layer chromatography, or high-performance liquid chromatography (HPLC) analysis. A purified or isolated polynucleotide (ribonucleic acid (RNA) or deoxyribonucleic acid (DNA)) is free of the genes or sequences that flank it in its naturally-occurring state. Purified also defines a degree of sterility that is safe for administration to a human subject, e.g., lacking infectious or toxic agents. In the case of tumor antigens, the antigen may be purified or a processed preparation such as a tumor cell lysate.
Similarly, by “substantially pure” is meant a nucleotide or polypeptide that has been separated from the components that naturally accompany it. Typically, the nucleotides and polypeptides are substantially pure when they are at least 60%, 70%, 80%, 90%, 95%, or even 99%, by weight, free from the proteins and naturally-occurring organic molecules with they are naturally associated.
A small molecule is a compound that is less than 2000 Daltons in mass. The molecular mass of the small molecule is preferably less than 1000 Daltons, more preferably less than 600 Daltons, e.g., the compound is less than 500 Daltons, 400 Daltons, 300 Daltons, 200 Daltons, or 100 Daltons.
The transitional term “comprising,” which is synonymous with “including,” “containing,” or “characterized by,” is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. By contrast, the transitional phrase “consisting or excludes” any element, step, or ingredient not specified in the claim. The transitional phrase “consisting essentially of” limits the scope of a claim to the specified materials or steps “and those that do not materially affect the basic and novel characteristic(s)” of the claimed invention.
Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All published foreign patents and patent applications cited herein are incorporated herein by reference. Genbank and NCBI submissions indicated by accession number cited herein are incorporated herein by reference. All other published references, documents, manuscripts and scientific literature cited herein are incorporated herein by reference. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.
Difficulty in transfecting molecules into non-adherent cells has plagued research and therapeutic, e.g., cell therapy, gene therapy, genetic alteration, for decades. A reason for the difficulty in transfecting such cells may be that non-adherent cells lack cell surface heparan sulfate proteoglycans, molecules are responsible for adhesion of cells to the extra-cellular matrix. Transfection methods such as electroporation and/or nucleofections have drawbacks in that they compromise the viability of cells, the ability of the cells to resume proliferation after treatment, and the function of the cells, e.g., immune activity of lymphocytes. The transfection compositions and methods described herein (Soluporation) do not have such drawbacks and therefore are characterized as having significant advantages over earlier methods of introducing cargo molecules into mammalian cells, e.g., difficult-to-transfect non-adherent/suspension cells.
The invention is based on the surprising discovery that compounds or mixtures of compounds (compositions) are delivered into the cytoplasm of eukaryotic cells by contacting the cells with a solution containing a compound(s) to be delivered (e.g., payload) and an agent that reversibly permeates or dissolves a cell membrane. Preferably, the solution is delivered to the cells in the faun of a spray, e.g., aqueous particles. (see, e.g., PCT/US2015/057247 and PCT/IB2016/001895, hereby incorporated in their entirety by reference). For example, the cells are coated with the spray but not soaked or submersed in the delivery compound-containing solution. Exemplary agents that permeate or dissolve a eukaryotic cell membrane include alcohols and detergents such as ethanol and Triton X-100, respectively. Other exemplary detergents, e.g., surfactants include polysorbate 20 (e.g., Tween 20), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), 3-[(3-chofarnidopropyl)dimethylammoni O]-2-hydroxy-1-propanesulfonate (CHAPSO), sodium dodecyl sulfate (SDS), and octyl glucoside.
An example of conditions to achieve a coating of a population of coated cells include delivery of a fine particle spray, e.g., the conditions exclude dropping or pipetting a bolus volume of solution on the cells such that a substantial population of the cells arc soaked or submerged by the volume of fluid. Thus, the mist or spray comprises a ratio of volume of fluid to cell volume. Alternatively, the conditions comprise a ratio of volume of mist or spray to exposed cell area, e.g., area of cell membrane that is exposed when the cells exist as a confluent or substantially confluent layer on a substantially flat surface such as the bottom of a tissue culture vessel, e.g., a well of a tissue culture plate, e.g., a microtiter tissue culture plate.
“Cargo” or “payload” are terms used to describe a compound, or composition that is delivered via an aqueous solution across a cell plasma membrane and into the interior of a cell.
In an aspect, delivering a payload across a plasma membrane of a cell includes providing a population of cells and contacting the population of cells with a volume of an aqueous solution. The aqueous solution includes the payload and an alcohol content greater than 5 percent concentration. The volume of the aqueous solution may be a function of exposed surface arca of the population of cells, or may be a function of a number of cells in the population of cells.
In another aspect, a composition for delivering a payload across a plasma membrane of a cell includes an aqueous solution including the payload, an alcohol at greater than 5 percent concentration, greater than 46 mM salt, less than 121 mM sugar, and less than 19 mM buffering agent. For example, the alcohol, e.g., ethanol, concentration does not exceed 50%.
One or more of the following features can be included in any feasible combination. The volume of solution to be delivered to the cells is a plurality of units, e.g., a spray, e.g., a plurality of droplets on aqueous particles. The volume is described relative to an individual cell or relative to the exposed surface area of a confluent or substantially confluent (e.g., at least 75%, at least 80% confluent, e.g., 85%, 90%, 95%, 97%, 98%, 100%) cell population. For example, the volume can be between 6.0×10−7 microliter per cell and 7.4×10−4 microliter per cell. The volume is between 4.9×10−6 microliter per cell and 2.2×10−3 microliter per cell. The volume can be between 9.3×10−6 microliter per cell and 2.8×10−5 microliter per cell. The volume can be about 1.9×10−5 microliters per cell, and about is within 10 percent. The volume is between 6.0×10−7 microliter per cell and 2.2×10−3 microliter per cell. The volume can be between 2.6 x 10 microliter per square micrometer of exposed surface area and 1.1×10−6 microliter per square micrometer of exposed surface area. The volume can be between 5.3×10-8 microliter per square micrometer of exposed surface area and 1.6×10−7 microliter per square micrometer of exposed surface area. The volume can be about 1.1×10−7 microliter per square micrometer of exposed surface area. About can be within 10 percent.
Confluency of cells refers to cells in contact with one another on a surface. For example, it can be expressed as an estimated (or counted) percentage, e.g., 10% confluency means that 10% of the surface, e.g., of a tissue culture vessel, is covered with cells, 100% means that it is entirely covered. For example, adherent cells grow two dimensionally on the surface of a tissue culture well, plate or flask. Non-adherent cells can be spun down, pulled down by a vacuum, or tissue culture medium aspiration off the top of the cell population, or removed by aspiration or vacuum removal from the bottom of the vessel.
Contacting the population of cells with the volume of aqueous solution can be performed by gas propelling the aqueous solution to form a spray. The gas can include nitrogen, ambient air, or an inert gas. The spray can include discrete units of volume ranging in size from, lnm to 100 μm, e.g., 30-100 μm in diameter. The spray includes discrete units of volume with a diameter of about 30-50 μm. A total volume of aqueous solution of 20μl can be delivered in a spray to a cell-occupied area of about 1.9 cm2, e.g., one well of a 24-well culture plate. A total volume of aqueous solution of 10 μl is delivered to a cell-occupied area of about 0.95 cm2, e.g., one well of a 48-well culture plate. Typically, the aqueous solution includes a payload to be delivered across a cell membrane and into cell, and the second volume is a buffer or culture medium that does not contain the payload. Alternatively, the second volume (buffer or media) can also contain payload. In some embodiments, the aqueous solution includes a payload and an alcohol, and the second volume does not contain alcohol (and optionally does not contain payload). The population of cells can be in contact with said aqueous solution for 0.1 10 minutes prior to adding a second volume of buffer or culture medium to submerse or suspend said population of cells. The buffer or culture medium can be phosphate buffered saline (PBS). The population of cells can be in contact with the aqueous solution for 2 seconds to 5 minutes prior to adding a second volume of buffer or culture medium to submerse or suspend the population of cells. The population of cells can be in contact with the aqueous solution, e.g., containing the payload, for 30 seconds to 2 minutes prior to adding a second volume of buffer or culture medium, e.g., without the payload, to submerse or suspend the population of cells. The population of cells can be in contact with a spray for about 1-2 minutes prior to adding the second volume of buffer or culture medium to submerse or suspend the population of cells. During the time between spraying of cells and addition of buffer or culture medium, the cells remain hydrated by the layer of moisture from the spray volume.
The aqueous solution can include an ethanol concentration of 5 to 30%. The aqueous solution can include one or more of 75 to 98% H2O, 2 to 45% ethanol, 6 to 91 mM sucrose, 2 to 500 mM KCl, 2 to 35 mM ammonium acetate, and 1 to 14 mM (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (HEPES). For example, the delivery solution contains 106 mM KCl and 27% ethanol.
The population of cells can include adherent cells or non-adherent cells. The adherent cells can include at least one of primary mesenchymal stem cells, fibroblasts, monocytes, macrophages, lung cells, neuronal cells, fibroblasts, human umbilical vein (HUVEC) cells, Chinese hamster ovary (CHO) cells, and human embryonic kidney (HEK) cells or immortalized cells, such as cell lines. In preferred embodiments, the population of cells comprises non-adherent cells, e.g., the % non-adherent cells in the population is at least 50%, 60%, 75%, 80%, 90%, 95%, 98%, 99% or 100% non-adherent cells. Non-adherent cells primary cells as well as immortalized cells (e.g., cells of a cell line). Exemplary non-adherent/suspension cells include primary hematopoietic stem cell (HSC), T cells (e.g., CD3+cells, CD4+cells, CD8+cells), natural killer (NK) cells, cytokine-induced killer (CIK) cells, human cord blood CD34+cells, B cells, or cell lines such as Jurkat T cell line.
The payload can include a small chemical molecule, a peptide or protein, or a nucleic acid. The small chemical molecule can be less than 1,000 Da. The chemical molecule can include MitoTrackerg Red CMXRos, propidium iodide, methotrexate, and/or DAPI (4′,6-diamidino-2-phenylindole). The peptide can be about 5,000 Da. The peptide can include ecallantide under trade name Kalbitor, is a 60 amino acid polypeptide for the treatment of hereditary angioedema and in prevention of blood loss in cardiothoracic surgery), Liraglutide (marketed as the brand name Victoza, is used for the treatment of type II diabetes, and Saxenda for the treatment of obesity), and Icatibant (trade name Firazyer, a peptidomimetic for the treatment of acute attacks of hereditary angioedema). The small-interfering ribonucleic acid (siRNA) molecule can be about 20-25 base pairs in length, or can be about 10,000-15,000 Da. The siRNA molecule can reduces the expression of any gene product, e.g., knockdown of gene expression of clinically relevant target genes or of model genes, e.g., glyceraldehyde-3phosphate dehydrogenase (GAPDH) siRNA, GAPDH siRNA-FITC, cyclophilin B siRNA, and/or lamin siRNA. Protein therapeutics can include peptides, enzymes, structural proteins, receptors, cellular proteins, or circulating proteins, or fragments thereof. The protein or polypeptide be about 100-500,000 Da, e.g., 1,000-150,000 Da. The protein can include any therapeutic, diagnostic, or research protein or peptide, e.g., beta-lactoglobulin, ovalbumin, bovine serum albumin (BSA), and/or horseradish peroxidase. In other examples, the protein can include a cancer-specific apoptotic protein, e.g., Tumor necrosis factor-related apoptosis inducing protein (TRAIL).
An antibody is generally be about 150,000 Da in molecular mass. The antibody can include an anti-actin antibody, an anti-GAPDH antibody, an anti-Src antibody, an anti-Myc ab, and/or an anti-Raf antibody. The antibody can include a green fluorescent protein (GFP) plasmid, a GLuc plasmid and, and a BATEM plasmid. The DNA molecule can be greater than 5,000,000 Da. In some examples, the antibody can be a murine-derived monoclonal antibody, e.g., ibritumomab tiuxetin, muromomab-CD3, tositumomab, a human antibody, or a humanized mouse (or other species of origin) antibody. In other examples, the antibody can be a chimeric monoclonal antibody, e.g., abciximab, basiliximab, ceniximab, infliximab, or rituximab. In still other examples, the antibody can be a humanized monoclonal antibody, e.g., alemtuzamab, bevacizumab, certolizumab pegol, daclizumab, gentuzumab ozogamicin, trastuzumab, tocilizumab, ipilimumamb, or panitumumab. The antibody can comprise an antibody fragment, e.g., abatecept, aflibercept, alefacept, or etanercept. The invention encompasses not only an intact monoclonal antibody, but also an immunologically-active antibody fragment, e.g., a Fab or (Fab)2 fragment; an engineered single chain Fv molecule; or a chimeric molecule, e.g., an antibody which contains the binding specificity of one antibody, e.g., of murine origin, and the remaining portions of another antibody, e.g., of human origin.
The payload can include a therapeutic agent. A therapeutic agent, e.g., a drug, or an active agent, can mean any compound useful for therapeutic or diagnostic purposes, the term can be understood to mean any compound that is administered to a patient for the treatment of a condition. Accordingly, a therapeutic agent can include, proteins, peptides, antibodies, antibody fragments, and small molecules. Therapeutic agents described in U.S. Pat. No.7,667,004 (incorporated herein by reference) can be used in the methods described herein. The therapeutic agent can include at least one of cisplatin, aspirin, statins (e.g., pitavastatin, atorvastatin, lovastatin, pravastatin, rosuvastatin, simvastatin, promazine HCl, chloroprornazine HCl, thioridazine HCl, Polymyxin B sulfate, chloroxine, benfluorex HCl and phenazopyridine HCl), and fluoxetine. The payload can include a diagnostic agent. The diagnostic agent can include a detectable label or marker such as at least one of methylene blue, patent blue V, and indocyanine green. The payload can include a fluorescent molecule. The payload can include a detectable nanoparticle. The nanoparticle can include a quantum dot.
The population of non-adherent cells can be substantially confluent, such as greater than 75 percent confluent. Confluency of cells refers to cells in contact with one another on a surface. For example, it can be expressed as an estimated (or counted) percentage, e.g., 10% confluency means that 10% of the surface, e.g., of a tissue culture vessel, is covered with cells, 100% means that it is entirely covered. For example, adherent cells grow two dimensionally on the surface of a tissue culture well, plate or flask. Non-adherent cells can be spun down, pulled down by a vacuum, or tissue culture medium aspiration off the top of the cell population, or removed by aspiration or vacuum removal from the bottom of the vessel. The population of cells can form a monolayer of cells.
The alcohol can be selected from methanol, ethanol, isopropyl alcohol, butanol and benzyl alcohol. The salt can be selected from NaCl, KCl, Na2HPO4, KH2PO4, and C2H3O2NH. In preferred embodiments, the salt is KCl. The sugar can include sucrose. The buffering agent can include 4-2-(hydroxyethyl)-1-piperazineethanesulfonic acid.
The present subject matter relates to a method for delivering molecules across a plasma membrane. The present subject matter finds utility in the field of intra-cellular delivery, and has application in, for example, delivery of molecular biological and pharmacological therapeutic agents to a target site, such as a cell, tissue, or organ. The method of the present subject matter comprises introducing the molecule to an aqueous composition to faun a matrix; atomizing the matrix into a spray; and contacting the matrix with a plasma membrane.
This present subject matter relates to a composition for use in delivering molecules across a plasma membrane. The present subject matter finds utility in the field of intra-cellular delivery, and has application in, for example, delivery of molecular biological and pharmacological therapeutic agents to a target site, such as a cell, tissue, or organ. The composition of the present subject matter comprises an alcohol; a salt; a sugar; and/or a buffering agent.
In some implementations, demonstrated is a permeabilisation technique that facilitates intracellular delivery of molecules independent of the molecule and cell type. Nanoparticles, small molecules, nucleic acids, proteins and other molecules can be efficiently delivered into suspension cells or adherent cells in situ, including primary cells and stem cells, with low cell toxicity and the technique is compatible with high throughput and automated cell-based assays.
The example methods described herein include a payload, wherein the payload includes an alcohol. By the term “an alcohol” is meant a polyatomic organic compound including a hydroxyl (—OH) functional group attached to at least one carbon atom. The alcohol may be a monohydric alcohol and may include at least one carbon atom, for example methanol. The alcohol may include at least two carbon atoms (e.g. ethanol). In other aspects, the alcohol comprises at least three carbons (e.g. isopropyl alcohol). The alcohol may include at least four carbon atoms (e.g., butanol), or at least seven carbon atoms (e.g., benzyl alcohol). The example payload may include no more than 50% (v/v) of the alcohol, more preferably, the payload comprises 2-45% (v/v) of the alcohol, 5-40% of the alcohol, and 10-40% of the alcohol. The payload may include 20-30% (v/v) of the alcohol.
Most preferably, the payload delivery solution includes 25% (v/v) of the alcohol. Alternatively, the payload can include 2-8% (v/v) of the alcohol, or 2% of the alcohol. The alcohol may include ethanol and the payload comprises 5, 10, 20, 25, 30, and up to 40% or 50% (v/v) of ethanol, e.g., 27%. Example methods may include methanol as the alcohol, and the payload may include 5, 10, 20, 25, 30, or 40% (v/v) of the methanol. The payload may include 2-45% (v/v) of methanol, 20-30% (v/v), or 25% (v/v) methanol. Preferably, the payload includes 20-30% (v/v) of methanol. Further alternatively, the alcohol is butanol and the payload comprises 2, 4, or 8% (v/v) of the butanol.
In some aspects of the present subject matter, the payload is in an isotonic solution or buffer.
According to the present subject matter, the payload may include at least one salt. The salt may be selected from NaCl, KCl, Na2HPO4, C2H3O2NH4 and KH2PO4. For example, KCl concentration ranges from 2 mM to 500 mM. In some preferred embodiments, the concentration is greater than 100 mM, e.g., 106 mM.
According to example methods of the present subject matter, the payload may include a sugar (e.g., a sucrose, or a disaccharide). According to example methods, the payload comprises less than 121 mM sugar, 6-91 mM, or 26-39 mM sugar. Still further, the payload includes 32 mM sugar (e.g., sucrose). Optionally, the sugar is sucrose and the payload comprises 6.4, 12.8, 19.2, 25.6, 32, 64, 76.8, or 89.6 mM sucrose.
According to example methods of the present subject matter, the payload may include a buffering agent (e.g. a weak acid or a weak base). The buffering agent may include a zwitterion. According to example methods, the buffering agent is 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid. The payload may comprise less than 19 mM buffering agent (e.g., 1-15 mM, or 4-6 mM or 5 mM buffering agent). According to example methods, the buffering agent is 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid and the payload comprises 1, 2, 3, 4, 5, 10, 12, 14 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid. Further preferably, the payload comprises 5 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid.
According to example methods of the present subject matter, the payload includes ammonium acetate. The payload may include less than 46 mM ammonium acetate (e.g., between 2-35 mM, 10-15 mM, ore 12 mM ammonium acetate). The payload may include 2.4, 4.8, 7.2, 9.6, 12, 24, 28.8, or 33.6 mM ammonium acetate.
The volume of aqueous solution performed by gas propelling the aqueous solution may include compressed air (e.g. ambient air), other implementations may include inert gases, for example, helium, neon, and argon.
In certain aspects of the present subject matter, the population of cells may include adherent cells (e.g., lung, kidney, immune cells such as macrophages) or non-adherent cells (e.g., suspension cells).
In certain aspects of the present subject matter, the population of cells may be substantially confluent, and substantially may include greater than 75 percent confluent. In preferred implementations, the population of cells may form a single monolayer.
According to example methods, the payload to be delivered has an average molecular weight of up to 20,000,000 Da. In some examples, the payload to be delivered can have an average molecular weight of up to 2,000,000 Da. In some implementations, the payload to be delivered may have an average molecular weight of up to 150,000 Da. In further implementations, the payload to be delivered has an average molecular weight of up to 15,000 Da, 5,000 Da or 1,000 Da.
The payload to be delivered across the plasma membrane of a cell may include a small chemical molecule, a peptide or protein, a polysaccharide or a nucleic acid or a nanoparticle. A small chemical molecule may be less than 1,000 Da, peptides may have molecular weights about 5,000 Da, siRNA may have molecular weights around 15,000 Da, antibodies may have molecular weights of about 150,000 Da and DNA may have molecular weights of greater than or equal to 5,000,000 Da. In preferred embodiments, the payload comprises mRNA.
According to example methods, the payload includes 3.0-150.0 μM of a molecule to be delivered, more preferably, 6.6-150.0 μM molecule to be delivered (e.g. 3.0, 3.3, 6.6, or 150.0 μM molecule to be delivered). In some implementations, the payload to be delivered has an average molecular weight of up to 15,000 Da, and the payload includes 3.3 μM molecules to be delivered.
According to example methods, the payload to be delivered has an average molecular weight of up to 15,000 Da, and the payload includes 6.6 μM to be delivered. In some implementations, the payload to be delivered has an average molecular weight of up to 1,000 Da, and the payload includes 150.0 μM to be delivered.
According to further aspects of the present subject matter, a method for delivering molecules of more than one molecular weight across a plasma membrane is provided; the method including the steps of: introducing the molecules of more than one molecular weight to an aqueous solution; and contacting the aqueous solution with a plasma membrane.
In some implementations, the method includes introducing a first molecule having a first molecular weight and a second molecule having a second molecular weight to the payload, wherein the first and second molecules may have different molecular weights, or wherein, the first and second molecules may have the same molecular weights. According to example methods, the first and second molecules may be different molecules.
In some implementations, the payload to be delivered may include a therapeutic agent, or a diagnostic agent, including, for example, cisplatin, aspirin, various statins (e.g., pitavastatin, atorvastatin, lovastatin, pravastatin, rosuvastatin, simvastatin, promazinc HCl, chloropromazinc HCl, thioridazine HCl, Polymyxin B sulfate, chloroxine, benfluorex HCl and phenazopyridine HCl), and fluoxetine. Other therapeutic agents include antimicrobials (aminoclyclosides (e.g. gentamicin, neomycin, streptomycin), penicillins (e.g., amoxicillin, ampicillin), glycopeptides (e.g., avoparcin, vancomycin), macrolides (e.g., erythromycin, tilmicosin, tylosin), quinolones (e.g., sarafloxacin, enrofloxin), streptogramins (e.g., viginiamycin, quinupristin-dalfoprisitin), carbapenems, lipopeptides, oxazolidinones, cycloserine, ethambutol, ethionamide, isoniazrid, para-aminosalicyclic acid, and pyrazinamide). In some examples, an anti-viral (e.g., Abacavir, Aciclovir, Enfuvirtide, Entecavir, Nelfinavir, Nevirapine, Nexavir, Oseltamivir Raltegravir, Ritonavir, Stavudine, and Valaciclovir). The therapeutic may include a protein-based therapy for the treatment of various diseases, e.g., cancer, infectious diseases, hemophilia, anemia, multiple sclerosis, and hepatitis B or C.
Additional exemplary payloads can also include detectable markers or labels such as methylene blue, Patent blue V, and Indocyanine green.
The methods described herein may also include the payload including of a detectable moiety, or a detectable nanoparticle (e.g., a quantum dot). The detectable moiety may include a fluorescent molecule or a radioactive agent (e.g., 125I).When the fluorescent molecule is exposed to light of the proper wave length, its presence can then be detected due to fluorescence. Among the most commonly used fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, p-phthaldehyde and fluorescamine. The molecule can also be detectably labeled using fluorescence emitting metals such as 152Eu, or others of the lanthanide series. These metals can be attached to the molecule using such metal chelating groups as diethylenetriaminepentacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA). The molecule also can be detectably labeled by coupling it to a chemiluminescent compound. The presence of the chemiluminescent-tagged molecule is then determined by detecting the presence of luminescence that arises during the course of chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester.
In additional embodiments, the payload to be delivered may include a composition that edits genomic DNA (i.e., gene editing tools). For example, the gene editing composition may include a compound or complex that cleaves, nicks, splices, rearranges, translocates, recombines, or otherwise alters genomic DNA. Alternatively or in addition, a gene editing composition may include a compound that (i) may be included a gene-editing complex that cleaves, nicks, splices, rearranges, translocates, recombines, or otherwise alters genomic DNA; or (ii) may be processed or altered to be a compound that is included in a gene-editing complex that cleaves, nicks, splices, rearranges, translocates, recombines, or otherwise alters genomic DNA. In various embodiments, the gene editing composition comprises one or more of (a) gene editing protein; (b) RNA molecule; and/or (c) ribonucleoprotein (RNP).
In some embodiments, the gene editing composition comprises a gene editing protein, and the gene editing protein is a zinc finger nuclease (ZFN), a transcription activator-like effector nuclease (TALEN), a Cas protein, a Cre recombinase, a Hin recombinase, or a Flp recombinase. In additional embodiments, the gene editing protein may be a fusion proteins that combine homing endonucleases with the modular DNA binding domains of TALENs (megaTAL). For example, megaTAL may be delivered as a protein or alternatively, a mRNA encoding a megaTAL protein is delivered to the cells.
In various embodiments, the gene editing composition comprises a RNA molecule, and the RNA molecule comprises a sgRNA, a crRNA, and/or a tracrRNA.
In certain embodiments, the gene editing composition comprises a RNP, and the RNP comprises a Cas protein and a sgRNA or a crRNA and a tracrRNA. Aspects of the present subject matter are particularly useful for controlling when and for how long a particular gene-editing compound is present in a cell.
In various implementations of the present subject matter, the gene editing composition is detectable in a population of cells, or the progeny thereof, for (a) about 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 24, 48, 60, 72, 0.5-2, 0.5-6, 6-12 or 0.5-72 hours after the population of cells is contacted with the aqueous solution, or (b) less than about 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 24, 48, 60, 72, 0.5-2, 0.5-6, 6-12 or 0.5-72 hours after the population of cells is contacted with the aqueous solution.
In some embodiments, the genome of cells in the population of cells, or the progeny thereof, comprises at least one site-specific recombination site for the Cre recombinase, Hin recombinase, or Flp recombinase.
Aspects of the present invention relate to cells that comprise one gene editing compound, and inserting another gene editing compound into the cells. For example, one component of an RNP could be introduced into cells that express or otherwise already contain another component of the RNP. For example, cells in a population of cells, or the progeny thereof, may comprise a sgRNA, a crRNA, and/or a tracrRNA. In some embodiments the population of cells, or the progeny thereof, expresses the sgRNA, crRNA, and/or tracrRNA. Alternatively or in addition, cells in a population of cells, or the progeny thereof, express a Cas protein.
Various implementations of the subject matter herein include a Cas protein. In some embodiments, the Cas protein is a Cas9 protein or a mutant thereof. Exemplary Cas proteins (including Cas9 and non-limiting examples of Cas9 mutants) are described herein.
In various aspects, the concentration of Cas9 protein may range from about 0.1 to about 25 μg. For example, the concentration of Cas9 may be about 1 μg, about 5 μg, about 10 μg, about 15 μg, or about 20 μg. Alternatively, the concentration of Cas9 may range from about 10 ng/μL to about 300 ng/μL; for example from about 10 ng/μL to about 200 ng/μl; or from about 10 ng/μL, to about 100 ng/μl, or from about 10 ng/μL to about 50 ng/μl.
In certain embodiments, the gene editing composition comprises (a) a first sgRNA molecule and a second sgRNA molecule, wherein the nucleic acid sequence of the first sgRNA molecule is different from the nucleic acid sequence of the second sgRNA molecule; (b) a first RNP comprising a first sgRNA and a second RNP comprising a second sgRNA, wherein the nucleic acid sequence of the first sgRNA molecule is different from the nucleic acid sequence of the second sgRNA molecule; (c) a first crRNA molecule and a second crRNA molecule, wherein the nucleic acid sequence of the first crRNA molecule is different from the nucleic acid sequence of the second crRNA molecule; (d) a first crRNA molecule and a second crRNA molecule, wherein the nucleic acid sequence of the first crRNA molecule is different from the nucleic acid sequence of the second crRNA molecule, and further comprising a tracrRNA molecule; or (e) a first RNP comprising a first crRNA and a tracrRNA and a second RNP comprising a second crRNA and a tracrRNA, wherein the nucleic acid sequence of the first crRNA molecule is different from the nucleic acid sequence of the second crRNA molecule.
In aspects, the ratio of the Cas9 protein to guide RNA may be 1:1, 1:2, 1:3, 1:4, 1:5, 1:6, 1:7, 1:8, 1:9, or 1:10.
In embodiments, increasing the number of times that cells go through the delivery process (alternatively, increasing the number of doses), may increase the percentage edit; wherein, in some embodiments the number of doses may include 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 doses.
In various embodiments, the first and second sgRNA or first and second crRNA molecules together comprise nucleic acid sequences complementary to target sequences flanking a gene, an exon, an intron, an extrachromosomal sequence, or a genomic nucleic acid sequence, wherein the gene, an exon, intron, extrachromosomal sequence, or genomic nucleic acid sequence is about 1, 2, 3, 4, 5, 6, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1-100, kilobases in length or is at least about 1, 2, 3, 4, 5, 6, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 1-100, kilobases in length. In some embodiments, the use of pairs of RNPs comprising the first and second sgRNA or first and second crRNA molecules may be used to create a polynucleotide molecule comprising the gene, exon, intron, extrachromosomal sequence, or genomic nucleic acid sequence.
In certain embodiments, the target sequence of a sgRNA or crRNA is about 12 to about 25, or about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 17-23, or 18-22, nucleotides long. In some embodiments, the target sequence is 20 nucleotides long or about 20 nucleotides long.
In various embodiments, the first and second sgRNA or first and second crRNA molecules are complementary to sequences flanking an extrachromosomal sequence that is within an expression vector.
Aspects of the present subject matter relate to the delivery of multiple components of a gene-editing complex, where the multiple components are not complexed together. In some embodiments, gene editing composition comprises at least one gene editing protein and at least one nucleic acid, wherein the gene editing protein and the nucleic acid are not bound to or complexed with each other.
The present subject matter allows for high gene editing efficiency while maintaining high cell viability. In some embodiments, at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, 99%, 1-99%, or more of the population of cells, or the progeny thereof, become genetically modified after contact with the aqueous solution. In various embodiments, at least about 10, 20, 30, 40, 50, 60, 70, 80, 90, 95, 99%, 1-99%, or more of the population of cells, or the progeny thereof, are viable after contact with the aqueous solution.
In certain embodiments, the gene editing composition induces single-strand or double-strand breaks in DNA within the cells. In some embodiments the gene editing composition further comprises a repair template polynucleotide. In various embodiments, the repair template comprises (a) a first flanking region comprising nucleotides in a sequence complementary to about 40 to about 90 base pairs on one side of the single or double strand break and a second flanking region comprising nucleotides in a sequence complementary to about 40 to about 90 base pairs on the other side of the single or double strand break; or (b) a first flanking region comprising nucleotides in a sequence complementary to at least about 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, or 90 base pairs on one side of the single or double strand break and a second flanking region comprising nucleotides in a sequence complementary to at least about 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, or 90 base pairs on the other side of the single or double strand break. Non-limiting descriptions relating to gene editing (including repair templates) using the CRISPR-Cas system are discussed in Ran et al. (2013) Nat Protoc. 2013 Nov.; 8(11): 2281-2308, the entire content of which is incorporated herein by reference. Embodiments involving repair templates are not limited to those comprising the CRISPR-Cas system.
In various implementations of the present subject matter, the volume of aqueous solution is delivered to the population of cells in the form of a spray. In some embodiments, the volume is between 6.0×10−7 microliter per cell and 7.4×104 microliter per cell. In certain embodiments, the spray comprises a colloidal or sub-particle comprising a diameter of 10 nm to 100 μm. In various embodiments, the volume is between 2.6×10−9 microliter per square micrometer of exposed surface area and 1.1×10−6 microliter per square micrometer of exposed surface area.
In some embodiments, the RNP has a size of approximately 100 Å×100 Å×50 Å or 10 nm×10 nm×5 nm. In various embodiments, the size of spray particles is adjusted to accommodate at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more RNPs per spray particle.
For example, contacting the population of cells with the volume of aqueous solution may be performed by gas propelling the aqueous solution to form a spray. In certain embodiments, the population of cells is in contact with said aqueous solution for 0.01-10 minutes (e.g., 0.1 10 minutes) prior to adding a second volume of buffer or culture medium to submerse or suspend said population of cells.
In various embodiments, the population of cells includes at least one of primary or immortalized cells. For example, the population of cells may include mesenchymal stem cells, lung cells, neuronal cells, fibroblasts, human umbilical vein (HUVEC) cells, and human embryonic kidney (HEK) cells, primary or immortalized hematopoietic stern cell (HSC), T cells, natural killer (NK) cells, cytokine-induced killer (CIK) cells, human cord blood CD34+ cells, B cells. Non limiting examples of T cells may include CD8+ or CD4+ T cells . In some aspects, the CD8+ subpopulation of the CD3± T cells arc used. CD8+ T cells may be purified from the PBMC population by positive isolation using anti-CD8 beads. In some aspects primary NK cells are isolated from PBMCs and GFP mRNA may he delivered by platform delivery technology (i.e., 3% expression and 96% viability at 24 hours). In additional aspects, NK cell lines, e.g., NK92 may be used.
Cell types also include cells that have previously been modified for example T cells, NK cells and MSC to enhance their therapeutic efficacy. For example: T cells or NK cells that express chimeric antigen receptors (CAR T cells, CAR NK cells, respectively); T cells that express modified T cell receptor (TCR); MSC that are modified virally or non-virally to overexpress therapeutic proteins that complement their innate properties (e.g. delivery of Epo using lentiviral vectors or BMP-2 using AAV-6) (reviewed in Park et al, Methods, 2015 August; 84-16.); MSC that arc primed with non-peptidic drugs or magnetic nanoparticles for enhanced efficacy and externally regulated targeting respectively (Park et al., 2015); MSC that are functionalised with targeting moieties to augment their homing toward therapeutic sites using enzymatic modification (e.g. Fucosyltransferase), chemical conjugation (eg. modification of SLeX on MSC by using N-hydroxy-succinimide (NHS) chemistry) or non-covalent interactions (eg. engineering the cell surface with palmitated proteins which act as hydrophobic anchors for subsequent conjugation of antibodies) (Park et al., 2015). For example, T cells, e.g., primary T cells or T cell lines, that have been modified to express chimeric antigen receptors (CAR T cells) may further be treated according to the invention with gene editing proteins and or complexes containing guide nucleic acids specific for the CAR encoding sequences for the purpose of editing the gene(s) encoding the CAR, thereby reducing or stopping the expression of the CAR in the modified T cells.
Aspects of the present invention relate to the expression vector-free delivery of gene editing compounds and complexes to cells and tissues, such as delivery of Cas-gRNA ribonucleoprotcins for genome editing in primary human T cells, hematopoietic stem cells (HSC), and mesenchymal stromal cells (MSC). In some example, mRNA encoding such proteins are delivered to the cells.
Various aspects of the CRISPR-Cas system are known in the art. Non-limiting aspects of this system are described, e.g., in U.S. Pat. Nos.9,023,649, issued May 5, 2015; U.S. Pat. No. 9,074,199, issued Jul. 7, 2015; U.S. Pat. No. 8,697,359, issued Apr. 15, 2014; U.S. Pat. No. 8,932,814, issued Jan. 13, 2015; PCT International Patent Application Publication No. WO 2015/071474, published Aug. 27, 2015; Cho et al., (2013) Nature Biotechnology Vol 31 No 3 pp 230-232 (including supplementary information); and Jinek et al., (2012) Science Vol 337 No 6096 pp 816-821, the entire contents of each of which are incorporated herein by reference.
Non-limiting examples of Cas proteins include Cas1, Cas1B, Cas2, Cas3, Cas4, CasS, Cash, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof. These enzymes are known; for example, the amino acid sequence of S. pyogenes Cas9 protein may be found in the SwissProt database under accession number Q99ZW2 and in the NCBI database as under accession number Q99ZW2.1. UniProt database accession numbers A0A0G4DEU5 and CDJ55032 provide another example of a Cas9 protein amino acid sequence. Another non-limiting example is a Streptococcus thermophilus Cas9 protein, the amino acid sequence of which may be found in the UniProt database under accession number Q03116.1. In some embodiments, the unmodified CRISPR enzyme has DNA cleavage activity, such as Cas9. In certain embodiments the CRISPR enzyme is Cas9, and may be Cas9 from S. pyogenes or S. pneumoniae. In various embodiments, the CRISPR enzyme directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. In some embodiments, a vector encodes a CRISPR enzyme that is mutated to with respect to a corresponding wild-type enzyme such that the mutated CRISPR enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A. In aspects of the invention, nickases may be used for genome editing via homologous recombination.
In certain embodiments, a Cas9 nickase may be used in combination with guide sequence(s), e.g., two guide sequences, which target respectively sense and antisense strands of the DNA target. This combination allows both strands to be nicked and used to induce NHEJ.
As a further example, two or more catalytic domains of Cas9 (RuvC 1, RuvC 11, and RuvC III) may be mutated to produce a mutated Cas9 substantially lacking all DNA cleavage activity. A D10A mutation may be combined with one or more of H840A, N854A, or N863A mutations to produce a Cas9 enzyme substantially lacking all DNA cleavage activity. In certain embodiments, a CRISPR enzyme is considered to substantially lack all DNA cleavage activity when the DNA cleavage activity of the mutated enzyme is less than about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or lower with respect to its non-mutated form. Other mutations may be useful;
where the Cas9 or other CRTSPR enzyme is from a species other than S. pyogenes, mutations in corresponding amino acids may be made to achieve similar effects.
In certain embodiments, a protein being delivered (such as a Cas protein or a variant thereof) may include a subcellular localization signal. For example, the Cas protein within a RNP may comprise a subcellular localization signal. Depending on context, a fusion protein comprising, e.g., Cas9 and a nuclear localization signal may be referred to as “Cas9” herein without specifying the inclusion of the nuclear localization signal. In some embodiments, the payload (such as an RNP) comprises a fusion-protein that comprises a localization signal. For example, the fusion-protein may contain a nuclear localization signal, a nucleolar localization signal, or a mitochondrial targeting signal. Such signals are known in the art, and non-limiting examples are described in Kalderon et al., (1984) Cell 39 (3 Pt 2): 499-509; Makkerh et al., (1996) Curr Biol. 6 (8):1025-7; Dingwall et al., (1991) Trends in Biochemical Sciences 16 (12): 478-81; Scott et al., (2011) BMC Bioinformatics 12:317 (7 pages); Omura T (1998) J Biochem. 123(6):1010-6; Rapaport D (2003) EMBO Rep. 4(10):948-52; and Brocard & Hartig (2006) Biochimica et Biophysica Acta (BBA)—Molecular Cell Research 1763(12):1565-1573, the contents of each of which are hereby incorporated herein by reference. In various embodiments, the Cas protein may comprise more than one localization signals, such as 2, 3, 4, 5, or more nuclear localization signals. In some embodiments, the localization signal is at the N-terminal end of the Cas protein and in other embodiments the localization signal is at the C-terminal end of the Cas protein.
In some embodiments, an enzyme coding sequence encoding a CRISPR enzyme is codon optimized for expression in particular cells, such as eukaryotic cells. The eukaryotic cells may be those of or derived from a particular organism, such as a mammal, including but not limited to human, mouse, rat, rabbit, dog, or non-human primate. In general, codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g. about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. Various species exhibit particular bias for certain codons of a particular amino acid. Codon bias (differences in codon usage between organisms) often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, among other things, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis.
Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. Codon usage tables are readily available, for example, at the “Codon Usage Database”, and these tables can be adapted in a number of ways. See Nakamura, Y., et al. “Codon usage tabulated from the international DNA sequence databases: status for the year 2000” Nucl. Acids Res. 28:292 (2000). Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge (Aptagen; Jacobus, Pa.), are also available. In some embodiments, one or more codons (e.g. 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more, or all codons) in a sequence encoding a CRISPR enzyme corresponding to the most frequently used codon for a particular amino acid.
In general, a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a CRISPR complex to the target sequence. In some embodiments, the degree of complementarity between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. In some embodiments, the degree of complementarily is 100%. Optimal alignment may be detel lined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). In some embodiments, a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In certain embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. The ability of a guide sequence to direct sequence-specific binding of a CRISPR complex to a target sequence may be assessed by any suitable assay. For example, the components of a CRISPR system sufficient to faint a CRISPR complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of the CRISPR sequence, followed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target polynucleotide sequence may be evaluated in a test tube by providing the target sequence, components of a CRISPR complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions.
CRISPR-Cas technology which facilitates genome engineering in a wide range of cell types is evolving rapidly. It has recently been shown that delivery of the Cas9-gRNA editing tools in the form of ribonucleoproteins (RNPs) yields several benefits compared with delivery of plasmids encoding for Cas9 and gRNAs. Benefits include faster and more efficient editing, fewer off-target effects, and less toxicity. RNPs have been delivered by lipofection and electroporation but limitations that remain with these delivery methods, particularly for certain clinically relevant cell types, include toxicity and low efficiency. Accordingly, there is a need to provide a vector-free e.g., viral vector-free, approach for delivering biologically relevant payloads, e.g., RNPs, across a plasma membrane and into cells. “Cargo” or “payload” are terms used to describe a compound, or composition that is delivered via an aqueous solution across a cell plasma membrane and into the interior of a cell.
The current subject matter relates to delivery technology that facilitates delivery of a broad range of payloads to cells with low toxicity. Genome editing may be achieved by delivering RNPs to cells using some aspects of the current subject matter. Levels decline thereafter until Cas9 is no longer detectable. The delivery technology per se does not deleteriously affect the viability or functionality of Jurkat and primary T cells. The current subject matter enables gene editing via Cas9 RNPs in clinically relevant cell types with minimal toxicity.
The transient and direct delivery of CRISPR/Cas components such as Cas and/or a gRNA has advantages compared to expression vector-mediated delivery. For example, an amount of Cas, gRNA, or RNP can be added with more precise timing and for a limited amount of time compared to the use of an expression vector. Components expressed from a vector may be produced in various quantities and for variable amounts of time, making it difficult to achieve consistent gene editing without off-target edits. Additionally, pre-formed complexes of Cas and gRNAs (RNPs) cannot be delivered with expression vectors.
In one aspect, the present subject matter describes cells attached to a solid support, (e.g., a strip, a polymer, a bead, or a nanoparticle). The support or scaffold may be a porous or non-porous solid support. Well-known supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present subject matter. The support material may have virtually any possible structural configuration. Thus, the support configuration may be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface may be flat such as a sheet, or test strip, etc. Preferred supports include polystyrene beads.
In other aspects, the solid support comprises a polymer, to which cells are chemically bound, immobilized, dispersed, or associated. A polymer support may be a network of polymers, and may be prepared in bead form (e.g., by suspension polymerization). The cells on such a scaffold can be sprayed with payload containing aqueous solution according to the invention to deliver desired compounds to the cytoplasm of the scaffold. Exemplary scaffolds include stents and other implantable medical devices or structures.
The present subject matter further relates to apparatus, systems, techniques and articles for delivery of payloads across a plasma membrane. The present subject matter also relates to an apparatus for delivering payloads such as proteins or protein complexes across a plasma membrane. The current subject matter may find utility in the field of intra-cellular delivery, and has application in, for example, delivery of molecular biological and pharmacological therapeutic agents to a target site, such as a cell, tissue, or organ.
In some implementations, an apparatus for delivering a payload across a plasma membrane can include an atomizer having at least one atomizer emitter and a support oriented relative to the atomizer. The method further comprises the step of atomizing the payload prior to contacting the plasma membrane with the payload.
The atomizer can be selected from a mechanical atomizer, an ultrasonic atomizer, an electrospray, a nebuliser, and a Venturi tube. The atomizer can be a commercially available atomizer. The atomizer can be an intranasal mucosal atomization device. The atomizer can be an intranasal mucosal atomization device commercially available from LMA Teleflex of NC, USA. The atomizer can be an intranasal mucosal atomization device commercially available from LMA Teleflex of NC, USA under catalogue number MAD300.
The atomizer can be adapted to provide a colloid suspension of particles having a diameter of 30-100 μm prior to contacting the plasma membrane with the payload. The atomizer can be adapted to provide a colloid suspension of particles having a diameter of 30-80 μm. The atomizer can be adapted to provide a colloid suspension of particles having a diameter of 50-The atomizer can include a gas reservoir. The atomizer can include a gas reservoir with the gas maintained under pressure. The gas can be selected from air, carbon dioxide, and helium. The gas reservoir can include a fixed pressure head generator. The gas reservoir can be in fluid communication with the atomizer emitter. The gas reservoir can include a gas guide, which can be in fluid communication with the atomizer emitter. The gas guide can be adapted to allow the passage of gas therethrough. The gas guide can include a hollow body. The gas guide can be a hollow body having open ends. The gas guide can include a hollow body having first and second open ends. The gas guide can be a hollow body having first and second opposing open ends. The diameter of the first open end can be different to the diameter of the second open end. The diameter of the first open end can be different to the diameter of the second open end. The diameter of the first open end can be greater than the diameter of the second open end. The first open end can be in fluid communication with the gas reservoir. The second open end can be in fluid communication with the atomizer emitter.
The apparatus can include a sample reservoir. The sample reservoir can be in fluid communication with the atomizer. The sample reservoir can be in fluid communication with the atomizer emitter. The gas reservoir and the sample reservoir can both be in fluid communication with the atomizer emitter.
The apparatus can include a sample valve located between the sample reservoir and the gas reservoir. The apparatus can include a sample valve located between the sample reservoir and the gas guide. The sample valve can be adapted to adjust the sample flow from the sample reservoir. The sample valve can be adapted to allow continuous or semi-continuous sample flow. The sample valve can be adapted to allow semi-continuous sample flow. The sample valve can be adapted to allow semi-continuous sample flow of a defined amount. The sample valve is adapted to allow semi-continuous sample flow of 0.5-100 μL. The sample valve can be adapted to allow semi-continuous sample flow of 100. The sample valve can be adapted to allow semi-continuous sample flow of 1 μL to an area of 0.065-0.085 cm2.
The atomizer and the support can be spaced apart. The support can include a solid support. The support can include a plate including sample wells. The support can include a plate including sample wells selected from 1, 6, 9, 12, 24, 48, 384, 1536 or more wells. Alternatively, the support comprises a plate, e.g., a scaled up configuration that can accommodate a monolayer with more cells than a microtiter plate. The solid support can be formed from an inert material. The solid support can be formed from a plastic material, or a metal or metal alloy, or a combination thereof. The support can include a heating element. The support can include a resistive element. The support can be reciprocally mountable to the apparatus. The support can be reciprocally movable relative to the apparatus. The support can be reciprocally movable relative to the atomizer. The support can be reciprocally movable relative to the atomizer emitter. The support can include a support actuator to reciprocally move the support relative to the atomizer. The support can include a support actuator to reciprocally move the support relative to the atomizer emitter. The support can include a support actuator to reciprocally move the support relative to the longitudinal axis of the atomizer emitter. The support can include a support actuator to reciprocally move the support transverse to the longitudinal axis of the atomizer emitter.
The longitudinal axis of the spray zone can be coaxial with the longitudinal axis or center point of the support and/or the circular well of the support, to which the payload is to be delivered. The longitudinal axis of the atomizer emitter can be coaxial with the longitudinal axis or center point of the support and/or the circular well of the support. The longitudinal axis of the atomizer emitter, the longitudinal axis of the support, and the longitudinal axis of the spray zone can be each coaxial. The longitudinal length of the spray zone may be greater than the diameter (may be greater than double) of the circular base of the spray zone (e.g., the area of cells to which the payload is to be delivered).
The apparatus can include a valve located between the gas reservoir and the atomizer. The valve can be an electromagnetically operated valve. The valve can be a solenoid valve. The valve can be a pneumatic valve. The valve can be located at the gas guide. The valve can be adapted to adjust the gas flow within the gas guide. The valve can be adapted to allow continuous or semi-continuous gas flow. The valve can be adapted to allow semi-continuous gas flow. The valve can be adapted to allow semi-continuous gas flow of a defined time interval. The valve can be adapted to allow semi-continuous gas flow of a one second time interval. The apparatus can include at least one filter. The filter can include a pore size of less than 10 μm. The filter can have a pore size of 10 μm. The filter can be located at the gas guide. The filter can be in fluid communication with the gas guide.
The apparatus can include at least one regulator. The regulator can be an electrical regulator. The regulator can be a mechanical regulator. The regulator can be located at the gas guide. The regulator can be in fluid communication with the gas guide. The regulator can be a regulating valve. The pressure within the gas guide can be 1.0-2.0 bar. The pressure within the gas guide can be 1.5 bar. The pressure within the gas guide can be 1.0-2.0 bar, and the distance between the atomizer and the support can be less than or equal to 31 mm. The pressure within the gas guide can be 1.5 bar, and the distance between the atomizer and the support can be 31 mm. The pressure within the gas guide can be 0.05 bar per millimeter distance between the atomizer and the support. The regulating valve can be adapted to adjust the pressure within the gas guide to 1.0-2.0 bar. The regulating valve cam be adapted to adjust the pressure within the gas guide to 1.5 bar. The or each regulating valve can be adapted to maintain the pressure within the gas guide at 1.0-2.0 bar. The or each regulating valve can be adapted to maintain the pressure within the gas guide at 1.5 bar.
The apparatus can include two regulators. The apparatus can include first and second regulators. The first and second regulator can be located at the gas guide. The first and second regulator can be in fluid communication with the gas guide. The first regulator can be located between the gas reservoir and the filter. The first regulator can be adapted to adjust the pressure from the gas reservoir within the gas guide to 2.0 bar. The first regulator can be adapted to maintain the pressure within the gas guide at 2.0 bar. The second regulator can be located between the filter and the valve.
The atomizer emitter can be adapted to provide a conical spray zone (e.g., a generally circular conical spray zone). The atomizer emitter can be adapted to provide a 30° conical spray zone. The apparatus further can include a microprocessor to control any or all parts of the apparatus. The microprocessor can be arranged to control any or all of the sample valve, the support actuator, the valve, and the regulator. The apparatus can include an atomizer having at least one atomizer emitter; and a support oriented relative to the atomizer; the atomizer can be selected from a mechanical atomizer, an ultrasonic atomizer, an electrospray, a nebuliser, and a Venturi tube. The atomizer can be adapted to provide a colloid suspension of particles having a diameter of 30-100 μm. The apparatus can include a sample reservoir and a gas guide, and a sample valve located between the sample reservoir and the gas guide. The sample valve can be adapted to allow semi-continuous sample flow of 10-100 μL. The atomizer and the support can be spaced apart and define a generally conical spray zone there between; and the distance between the atomizer and the support can be approximately double the diameter of the circular base of the area of cells to which molecules are to be delivered; the distance between the atomizer and the support can be 31 mm and the diameter of the circular base of the area of cells to which molecules are to be delivered can be 15.5 mm. The apparatus can include a gas guide and the pressure within the gas guide is 1.0-2.0 bar. The apparatus can include at least one filter having a pore size of less than 10 μm.
The aqueous solution and/or composition can be saponin-free.
The details of one or more variations of the subject matter described herein are set forth in the accompanying drawings and the description below. Other features and advantages of the subject matter described herein will be apparent from the description and drawings, and from the claims.
Optimization of T cell culture conditions for maximal efficiency of mRNA delivery using the vector-free reversible permeabilization method is described below. The vector-free method for intracellular delivery of macromolecules and nucleic acids described herein has demonstrated success in facilitating the delivery of gene-editing tools such as CRISPR/Cas9 and mRNA to mammalian cells such as primary human immune cells. Culture conditions for efficient transfer of mRNA to human T cells using the vector-free delivery platform were determined.
Considerable differences exist in the ex vivo activation of human lymphocytes amongst clinical groups and T-cell engineering companies. There is no single standardised protocol for expansion of primary human T cells, therefore, a comprehensive evaluation of culture media, additives, activation methods and timing schedules was undertaken to identify the optimal ex vivo culturing conditions that promote maximal efficiency transfer of mRNA using the vector-free reversible permeabilization method technology. Herein, the cell isolation protocol and the results/conclusions of each experiment undertaken is described.
To address suspension cells (i.e., non-adherent cells), a centrifugation step was developed as part of the delivery process. This step was developed to enable formation of an exposed monolayer of suspension cells. The centrifugation step allows for both formation of the monolayer and removal of the supernatant in one step. In contrast, with adherent cells, the cells were already in monolayer formation and medium were removed by pipetting.
Cell culture and transfection. Human peripheral blood mononuclear cells (PBMC) were recovered by centrifugation over a Percoll gradient from Leuko Pak (AllCells Alameda, CA). CD3+ enriched lymphocytes were isolated by magnetically activated cell sorting using CD3 Microbeads (Miltenyi). Cells were cryopreserved in 10% dimethyl sulphoxide (DMSO) and foetal bovine serum (FBS). Following initial thawing from stock aliquots, CD3′ T cells were cultured in human recombinant interleukin-2 (IL-2) with primary and co-stimulatory antibody activation using various protocols (see below) in a humidified tissue culture incubator at 37° C. and 5% CO2.
Delivery procedure. Activated T cells were seeded at 1.5×106 cells per well of a 96-well filter plate (Acroprep, 1.2 μm Supor membrane; Pall, USA). Media was removed from the wells by centrifugation at 300×g for 5 min. 7 μl of delivery solution (32 mM sucrose, 12 mM potassium chloride, 12 mM ammonium acetate, 5 mM HEPES and 27% ethanol in molecular grade water (all from Sigma-Aldrich)) containing 4 μg GFP mRNA was then sprayed into each well using the vector-free delivery spray instrument. The atomizer used in the instrument was a MAD Nasal™ intranasal mucosal atomization device (Wolfe Tory Medical Inc, Salt Lake City, USA). The atomizer was held on a retort stand at 26 mm above the bottom of the well and was connected to a 6 bar compressor (Circuit Imprime Francais, Bagneux Cedex, France) via polyurethane tubing (6 mm outside diameter, 4 mm inside diameter; SMC, Tokyo, Japan). The delivery solution containing the cargo was pipetted into a delivery port located at the top of the atomizer and the spray was generated at 1.5 Bar using a spray actuator button (SMC, Tokyo, Japan). Following delivery, the cells were incubated in this solution for 2 min prior to the addition of 50 μl Stop Solution (0.5× PBS). Thirty seconds later T cell media was added (100 μl) and cells were allowed to recover at 37° C. and 5% CO2 overnight. Uptake and viability were assessed at 24h post-delivery.
Cell viability, FACS Sample Preparation and Analysis. To assess cell viability following the vector-free method of delivery, 7-Aminoactinomycin D (7-AAD) (Sigma) was used to stain the cells. Briefly, cells were in washed in PBS +1% foetal bovine serum (FACS buffer) followed by incubation with 7-AAD (1:40 for 5-10 min protected from light at room temperature), followed by resuspension in PBS +1% FBS (FACS buffer). Samples were processed on the BD Accuri C6 flow cytometer (Becton Dickinson, USA) and data was analysed using the C6 software. Cell debris was excluded from whole cells using forward and side scatter parameters. Single cells were selected by excluding doublets in the FSC height vs FSC are plot. GFP expression was analysed on gated viable cells.
Four media for T cell culture and expansion were evaluated using mRNA, e.g., model cargo GFP mRNA, as cargo and GFP expression as an indicator of successful culture methodology. cRPMI was tested which is a serum-containing media typically used in the culture of primary immune cells. However, as serum is a highly variable supplement in cell-culture media, three serum-free and xeno-free expansion media, optimised for the in vitro culture of human T cells were also evaluated.
cRPMI was prepared using RPMI, heat-inactivated fetal bovine serum (FBS) (10% v/v), penicillin-streptomycin, L-glutamine and supplemented with IL-2 (100 U/ml). cRPMI was utilised as culture medium in experiments that assessed the performance of various T-cell proliferation protocols. The first proliferation protocol tested was ImmunoCultTM Human CD3/CD28 T-cell Activator which consists of a soluble tetrameric antibody complex that bind CD3 and CD28 cell surface ligands on the T lymphocytes. It was evaluated alongside an alternative method of activation which use “feeder” cells as a means of presenting antigen to the T cell receptor (TCR) to induce proliferation of the T cell (
T Cell Activation Using PBMC or A549 as Feeder Cells
Autologous PBMC were transferred to the tissue culture plate. After 2 hr incubation, the supernatant was removed leaving the adhered monocytes. T cells cultured in cRPMI were added to the plate and allowed to co-incubate with the monocytes for several days. In a similar protocol, the A549 cell line was left to adhere for up to 2 h. Medium was removed and T cells were added to the plate and left to co-incubate prior to delivery of mRNA using the vector-free delivery technology. Uptake efficiencies using feeder cells were variable both inter and intra-experiment (
T cells are activated using methods known in the art, e.g., antibodies that bind to cell surface proteins such as CD3 and/or CD28, feeder cells, and/or magnetic beads comprising immunostimulatory molecules. For example, Dynabeads® were examined as an alternative to ImmunoCult™ Human CD3/CD28 T-cell Activator. Dynabeads® are superparamagnetic beads coated with antibodies against human CD3 and CD28 that provide the primary and co-stimulatory signals necessary for T cell activation and expansion. The bead-to-cell ratio recommended is 1:1, however, another condition using 3 beads per cell was also used to assess whether more efficient and rapid expansion could positively affect uptake of mRNA into T cells using the Soluporation delivery method. Increasing the bead-to-cell ratio significantly improved percentage uptake (
Cell-compatible culture media are used in the delivery methods. For example, Prime-XV (Irvine Scientific) is a first serum-free and animal component free media that was tested with vector-free delivery technology. Based on positive data observed using Dynabeads at a 3:1 bead to cell ratio (
Although delivery to T cells cultured in Prime XV did improve uptake of mRNA using the vector-free technology, it was associated with cell-handling issues, e.g., removing the cells from culture 24 h after initial seeding and recovery of cells from the Dynabeads upon washing (
In some examples, the cell culture media was supplemented with a higher concentration of IL-2 (200U/ml instead of 100 U/ml) to enhance the rate of proliferation (Tumeh P, et al., J Immunother 2010. 33(6): 759-768 and Besser M J, et al., Cytotherapy 2009. 11:206-217).
Immunocult™-XF Expansion Medium (StemCell Technologies) was evaluated. Like Prime XV, it is also a serum-free, xeno-free T cell culture medium. In this example, T cells were cultured in Immunocult Expansion Medium and activated using Dynabeads® bead to cell ratio of 3 to 1. GFP mRNA was delivered to the cells at day 1 and day 2 post-activation and assessed for uptake 24 h later (
Cells are activated for between 15 to 21 hr, with 19 hr being preferred.
A preferred “window” for delivery post-activation after addition of Dynabeads was identified. mRNA was delivered using the vector-free technology at several time points. Optimal GFP expression was observed when mRNA payload, e.g., model payload GFP mRNA, was delivered at 19 h post-activation compared with 17 h and 21 h (
T cell Activation Using TransAct
T cell TransAct™ (Miltenyi) is a colloidal reagent consisting of a nanomatrix conjugated to CD3 and CD28 agonist which provide signals for activation and expansion of T cells. It provides benefits over Dynabeads0 as excess reagent can be removed by centrifugation without the need for magnetic separation and the beads from the cells and all the subsequent washing. Thus, this reagent was evaluated over a three-day period using Immunocult as the culture medium to determine the preferred day for delivery of mRNA by the vector-free delivery technology described herein. TransAct initiates T cell proliferation less aggressively than Dynabeads. Therefore, optimum delivery of mRNA to T cells was observed 24 h later than that demonstrated using bead activation, however, this was accompanied by an enhancement in transfection efficiency (
TexMACS (Miltenyi Biotech) was also tested as an alternative serum-free medium for T-cell culture. This T cell stimulation and expansion reagent was useful but not routinely used going forward (
The benefit for delivery to allow cells to recover overnight before addition of activation reagent compared with adding the recovery agent immediately after thawing without a recovery period was evaluated. Upon thawing of T cells from liquid nitrogen storage, cells were left to recover overnight in culture medium alone before the addition of activation reagent. This step resulted in a 30% improvement in transfection efficiency. In some examples, fresh primary non-adherent cells are used in the method; in other examples, primary non-adherent cells are frozen, e.g., for storage, and then thawed prior to the payload deliver method. The method may thus optionally include a freeze/thaw step of primary non-adherent cells. These data indicate that a recovery period (after thawing) prior to activation is useful.
Cells were cultured in Immunocult Expansion medium at various seeding densities (1×106/ml and 5×106 /ml) prior to the vector-free delivery. The density at which cells are cultured prior to Soluporation is between 1×5×106/mL. Higher seed number led to an enhancement in uptake efficiency (
Zinc influx can support T cell activation (Yu M, et al., J. Exp. Med. 208 (4) :775-785) but may also improve transfection of nucleic acid (Niedzinski E J, et al. Mol Ther 2003 7(3): 396-400). Zinc improved T cell proliferation in two independent experiments (
Optimization of T Cell Culture Conditions for Maximal Efficiency of mRNA Delivery
Evaluation of multiple culture media, activation methods, supplementation and time courses has resulted in a preconditioning protocol that maximises the transfection efficiency of mRNA, e.g., the model payload GFP mRNA, to human primary T cells using the vector-free delivery technology. In this evaluation, cells were cultured in Immunocult™ T Cell Expansion Medium supplemented with 200 U/ml of IL-2 at a density of 5×106 /ml. Cells were left to recover overnight post-thaw before the addition of 1×T cell TransAct™ (Miltenyi) for 48 h prior to vector-free delivery of nucleic acid.
Human peripheral blood mononuclear cells (PBMC) were recovered by centrifugation over a Percoll gradient from Leuko Pak (AilCells Alameda, Calif.). CD4 enriched T cells were isolated by negative selection to recover a purified population using anti-CD8 microbeads and the flow-through was collected from an LD column (Miltenyi). Cells were cultured in standard cell culture media, e.g., complete RPMI using RPMI basal medium, heat-inactivated fetal bovine scrum (FBS) (10% v/v), penicillin-streptomycin, L-glutaminc and supplemented with IL-2 (200 U/ml). Cells were left to recover for 4 hours before the addition Dynabeads® at a bead to cell ratio of 3 to 1. mRNA was delivered to the cells at day 1 post-activation and assessed for uptake 24 h later. Multiple hits in this cell type achieved higher uptake efficiency, >30% (
T cells were enriched from PBMC cultured in X-VIVO 15 supplemented with 2mM GlutaMAX, 10 mM HEPES and 5% Human AB Serum and 250 IU/ml IL-2. Cells were seeded at a density of 1×106/mL and supplemented with anti-CD3 and anti-CD28 antibodies (Miltcnyi) prior to culture. mRNA, e.g. test payload GFP mRNA, was delivered to the cells by soluporation at either day 2 or day 3 post-initiation and assessed for uptake 24 h later (
A cell monolayer is a culture in which cells are oriented in a single layer on substrate. The substrate is generally a plate, e.g., a microtiter plate, a flask, Petri dish, membrane, or filter upon which the cells lie. In cell culture, a monolayer refers to a layer of cells in which cells are substantially side by side and often touching each other on the same surface. The cells are adherent cells (cells that attach to a substrate) or non-adherent cells (cells that float or are suspended in culture media). Adherent cells grow on a substrate, attach, and thereby form a monolayer. A monolayer can also be made from non-adherent or “suspension cells”. The terms “non-adherent cells” and “suspension cells” are used interchangeably herein.
A number of techniques may be employed to make a cell monolayer from non-adherent or suspension cells prior to delivery of a payload to the cells. Such techniques include allowing a culture suspension cells to settle on substrate, centrifugation, exposure to a vacuum, exposure to positive pressure, use of magnetic T -cell activation beads and/or deposition onto a membrane (e.g., the use of a transwell insert system, described below.)
In order to form a monolayer of suspension cells that would allow the cells to be presented optimally to the spray, a transwell insert system was used. Cells were seeded at 1×106 in 400 μl per insert and the media was removed by placing the transwell insert (Greiner bio-one; CAT# 655640; 12 Well ThinCert; PET 0.4 μm) into a device that allowed a vacuum to be applied to the bottom of the insert (between −0.5 bar and −0.65 bar; see
Permeable membranes that allow filtering of culture media are also useful to generate cell monolayers. Such membranes include cellulose nitrate membranes, cellulose acetate or PES membranes.
Such a membrane-based system was assessed to create a suspension cell monolayer. 96-well filter bottomed plates provide a 96-well format with a filter bottom to the well. The Pall Supor filter plate (AcroPrep Advance; PES CAT# 8039) was assessed. 1×106 human primary T cells were seeded in 100 μl per well and the plate centrifuged at 300×g for 5 min. Once the media was removed by centrifugation, and the remaining cells formed a monolayer, the plate was placed within the Solupore device and cells sprayed with delivery solution containing mRNA. Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated for 2 hours before the process was repeated. At the end of this spray the cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytornetry. GFP expression levels of 52% ±3.6 across 5 donors and 5 experiments was achieved with a viability of 97% ±3.3 (
Alternative membrane filter systems may be used for generation of a cell monolayer of non-adherent cells. For example, an alternative filter plate with 0.4 μm hydrophilic PCTE filter was obtained from Agilent technologies. Human primary T cells were seeded at 2.5×105 cells per 100 gl per well and centrifuged at 350×g for 2 min. Once the media was removed and the cell monolayer formed, the plate was placed within the Solupore device and cells sprayed with delivery solution containing a test payload such as GFP mRNA. Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated for 2 hours before the process was repeated. At the end of this spray the cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. GFP expression levels of 72% ±5 was achieved with a viability of 75.0% ±3.5 (
The method for removal of media from the cells was also addressed. Using the filter plates, centrifugation, vacuum pressure and positive pressure were assessed. 1×106 human primary T cells were seeded per well in a 96-well filter plate (Pall; Supor, 1.2 gm; CATtt 8039). The media was removed by either centrifugation at 300×g for 5 min or by vacuum pressure (−120 mBar, 30 s; see
An alternative method combines the use of the T cell activation beads (e.g., DynaBeads 3:1 ratio) and a magnet. After overnight activation, the T cells (bound to the DynaBeads) were seeded in a 96-well plate. A magnet was placed underneath the wells and the media removed by pipette. The magnet holds the beads and cells in place while the media is removed. mRNA was then delivered by Soluporation. GFP expression was detected 24 hr later by fluorescence microscopy.
mRNA Delivery to MSCs
To confirm delivery to cells in a monolayer, mesenchymal stromal cells (either primary human or iPSC-derived) were seeded in 96-well plates so that by 24 hrs the confluency was 80-90%.
Delivery of mRNA, e.g., test payload/cargo GFP mRNA, to BM-MSCs and iPSC-MSCs was evaluated. The delivery of various cargo compounds such as 10 kDa dextran to primary human BM-MSCs using a vector-free method for intracellular delivery involving reversible peruieabilization was previously reported (O'Dea S, et al., PLoS One. 2017. 30; 12(3):e0174779). A method for delivery of functional molecules such as mRNA was also evaluated. A reporter GFP mRNA was used to evaluate mRNA delivery efficiency to BM-derived and iPSC-derived MSCs.
Multiple treatments, e.g., three doses of GFP mRNA, were delivered to BM-MSCs and iPSC-MSCs over 2 days. Fluorescence microscopy confirmed expression of GFP protein in cells 24 hr following delivery of the final dose of mRNA (
The Mucosal Atomization Device (MAD Nasal™) spray head, used to atomize the payload solution dispenses volume of milliliters while soluporation works with micro-litres volumes. The use of a microliter volume atomizer/droplet delivery system is preferable.
Alternative spray heads were investigated for two main purposes: increasing the uptake and improving reproducibility across replicates (intra-experiment) and across experiments (inter-experiment). An assessment of alternative atomiser devices was undertaken to find which was optimal for mRNA delivery to T cells. The atomiser allows the application of the delivery solution in dropletised fault to the cell monolayer. In addition to identification of the atomiser, a controller device was designed and built which allowed fine control of the atomisation process. A variety of parameter sets were tested to find the optimal parameters for delivery of mRNA to T-cells.
The results indicated that a microliter volume delivery device such as the Ari Mist nebuliser and 180 kHz ultrasonic nebuliser gave comparable uptake and reproducibility while cell viability was slightly higher with Ari Mist. Such a microliter volume delivery device such as the Ari Mist head was preferred and can be incorporated into an automated solution since it is smaller in size, easier to handle and does not require a power box to operate. Other units such as the Burgener nebulization technology (U.S. Pat. No. 6,634,572, hereby incorporated by reference) also was suitable for the scaling up of soluporation. Taken together, the Ari Mist and other Burgener nebulizers were used moving forward for automation and scaling.
A cell membrane pet teabilizing solution can be delivered onto a monolayer of cells using a variety of methods. For example, the permeabilizing solution can be atomized using ultrasonication or it can be nebulized using a pneumatic nebulizer.
Both air-assisted ultrasonication and pneumatic nebulization were tested as delivery methods. A total of eight different spray heads were tested: three ultrasonic heads namely 60 KHz (Sonaer), 130 kHz (Sonaer) and 180 kHz (Sonotek Echo) and five pneumatic nebulizers namely Ari Mist, X-175, PFA 250, T2100 and Peek Mira Mist (Burgener Research)
Ultrasonication tests were performed at 60 kHz, 130 kHz, and 180 kHz. Liquid can be driven to an ultrasonic nozzle by a pumping system, and it can be atomized into a fine mist spray using high frequency sound vibrations.
A curtain of gas (air) can assist the process. An auxiliary piece called shaper is mounted around the ultrasonic head and the function of the air is to shape the mist of liquid ultrasonicated. For example, the air had the dual function of shaping the spray as well as promoting the payload to enter the cells. This was possible because the air fed through the shaper was at pressure beyond that used for shaping function.
Testing with the ultrasonic nebulizer yielded results useful for delivery of caro/payload to mammalian cells, e.g., non-adherent cells. Up to 60% Dextran-Alexa488 (model cargo) was delivered to U2OS cells using the 180 kHz ultrasonic head (
Piezoelectric transducers can be used to impart electrical input into mechanical energy in the form of vibrations, which created capillary waves in the liquid when introduced into the nozzle, and resulted in atomization of the liquid. Each ultrasonic probe worked at a given resonant frequency. The operating frequency can determine the size of the liquid droplets generated. The size of the droplets can also be affected to a lesser extent by the power at which the ultrasonic probe is operated. An ancillary air stream can be used to help control and shape the spray.
An exemplary ultrasonic spray emitter generates a fine spray, with narrow size distribution of the droplets which in turn results in even deposition of the delivery solution and payload onto cells. Reducing the volume delivered and reducing the ethanol concentration, e.g., with respect to the preferred parameters evaluated for the MAD nasal spray head, improved delivery efficiency and improved viability with the ultrasonic spray head.
Additional nebulizers to generate droplets (microliter volume) were tested such as Ari Mist, Peek Mira Mist, T2100, X175 and PFA250 nebulizer (Burgener Research). These exemplary nebulizers operate on compressed gases and require a pump to supply the sample solution. These exemplary atomizers have two parallel channels, one for the gas (air) and the other one for the liquid to be nebulized. Both paths end at the tip of the nebulizer with an orifice for the gas and an exit for the liquid. The gas flow can draw the liquid into the gas stream. The impact with the gas molecules can break the liquid into small droplets, resulting in nebulization.
The Burgener nebulizers (U.S. Pat. No. 6,634,572) tested differ in inner diameter, material and optimal flow rate. In preliminary tests, the nebulizers gave comparable expression of cargo mRNA. Characterisation of the droplet size revealed droplets ranging from 1-20 μm, with the peak number of droplets in the range of 5-7 μm. The average particle size as defined by the Sauter mean (D32) dimeter is 13 μm [(see http://www.burgener.com/EnhancedData.html)] Amongst the suite of Burgener's nebulizers tested the Ari Mist was chosen as the preferential spray head based on several factors: uptake and viability were good, its specs (optimal flow-rate, inner diameter) matched the characteristics of the pumping system, its inner diameter (225 μm) was small enough to handle low volumes of liquid without the inconvenience of clogging.
The Certus Flex liquid dispensing instrument was equipped with an 8 channel dispensing head (Cat. # D196057) and two valve sizes (0.10 nozzle diameter, 0.03 travel (Cat. # 21765) and 0.15 nozzle diameter, 0.03 travel (Cat. # 21766). Each channel is individually controlled using the Certus proprietary software and electronics. The Certus Flex enables contactless dispensing of liquid and large molecules using Gyger micro valve technology and air pressure control. Volumes in the nano litre (n1) range can be delivered with high precision (100 nl with CV 5%; CV represents coefficient of variation or relative standard deviation).
Delivery mRNA to T cells through the generation of small droplets in the nanoliter (nl) to μl size range was examined to evaluate the feasibility of delivering mRNA to T-cells using the Certus Flex microfluidic platform.
CD3+ T-cells were activated using, e.g., either Dynabeads or TransAct. Cells were seeded at 1.5×106 cells per well of a 96-well filter plate (PES). The plate was centrifuged, e.g., for 5 mins at 300 g to remove the cell culture medium. Delivery solution was dispensed to each well through Channel 1 with the parameters listed in Table 1. A total volume of microliter amounts, e.g., 2 or 7 was delivered in droplets ranging in volume from 7 to 0.08 μl. The volume of the droplet was determined by the number of drops dispensed into the well.
The results indicate that cell viability was comparable to untreated cells using this system. No delivery of GFP mRNA was observed using this system. This was seen across all parameters tested (
A test rig was built to control the critical spray parameters and enable mechanisation of the spray. The plate containing the cell suspension was centrifuged prior to being placed on the test rig. The delivery solution containing the payload was loaded into the elveflow fluidic reservoir or a syringe system. Fluidic control of the delivery solution containing the payload was brought about either using a pinch valve or using a micro valve. Addition of the stop and culture medium was done manually.
Fluidic control of the delivery solution containing the payload was brought about using two systems, an elveflow-pinch valve system and a syringe-micro valve system. The syringe-micro valve system was shown to have benefit over the elveflow-pinch valve system.
a) Fluidic control of the delivery solution containing the payload
(i) Elveflow-Pinch Valve
Elveflow refers to a microfluidic reservoir which was used with a 1.5 ml Eppendorf tube or 50 ml falcon tube depending on the sample reservoir size required (Elvesys, Innovation centre, 83 avenue Philippe Auguste, 75011, Paris, FRANCE). Pinch valve can refer to any pinch valve where an example is the Electronic Clippard pinch valve (Clippard, 7390 Colerain Avenue, Cincinnati, Ohio 45239, USA) The fluidic control can be achieved by fluid control system that can apply a constant pressure to an elveflow fluidic reservoir to drive the fluid through a pinch valve (
The valve can be activated by a metal—oxide—semiconductor field-effect transistor (MOS FET) which can be controlled by a microprocessor.
(ii) Syringe-micro valve
b) Fluidic control of the air
Air pressure is optionally controlled by solenoid valve.
c) Electronics to control spray actuation
To enable electronically controlled spray actuation, a system was designed using a microprocessor based development board to allow easy development of time controlled sequences. The development board used the microprocessor, e.g., PIC16F1619. The spray actuation time and fluid delivery time can be manipulated through the development board's interface software. The microprocessor development board enables pulsing of the nebulizer spray.
This system was then upgraded to utilise the high speed and repeatable PLC technology (programmable logic controller) to better align with industry standards and to serve as proof of concept for the automated Solupore™ technology (which is based on ultra-high-speed Programmable Logic Controller (PLC) technology). The Test Rig controller consisted of a PLC with a Gyger controller and a program which communicates between the two pieces of hardware. There is operator interaction to the hardware via a momentary push button.
d) Alignment of the spray head
A sprayhead such as the Afi Mist nebulizer parallel path design produces a spray which is off centre from the nebulizer tip. Using a custom spray head holder equipped with a goniometer, the alignment of the spray head can be adjusted.
Identification of Optimal Parameters for Delivery of mRNA into T-Cells
Work was carried out to characterise and optimise the spray with the three ultrasonic heads and Ari Mist head. The character of the various sprays was assessed using high speed camera recording. The force of the spray experienced by the cell monolayer was detennined by force sensor analysis. In some cases, the volume delivered into the wells of a 96 well plate was assessed using a colorimetric assay
For the optimisation study the following parameters were tested, in the ranges indicated:
a) Air pressure: 0.5-2 bar
b) Volume delivered: 1-7 μl
c) Height of atomiser to target area: 26 and 31 mm
d) Length of spray actuation: 50-900 ms
e) Flow rate: 1-20 μUs
f) Power of ultrasonic probe: 40-80%
g) Spray head: Ari Mist, Ultrasonic 60 kHz, Ultrasonic 130 kHz, Ultrasonic 180 kHz Numerous sets of parameter combinations were tested with the three ultrasonic probes as well as with the Ari Mist nebulisers, using EGFP mRNA as the payload.
All sets of parameters resulted in GFP expression, with uptake varying from 5% to 30%.
Amongst the ultrasonic emitters, 180 kHz proved to be more effective compared to the 130 kHz and 60 kHz ultrasonic heads in delivering payloads to T-cells. The test results indicated that payloads had been delivered to T-cells successfully, at an efficiency of approximately 15-28%, with high level of consistency between replicates (±1%). The health of the cells was maintained following delivery (85% relative viability).
Uptake and reproducibility obtained with Ari Mist, 180 kHz ultrasonic and Mad Nasal spray heads was compared. Results are presented in the longitudinal data plots for Ari Mist, 180 kHz ultrasonic and Mad Nasal spray heads (
Improved reproducibility was observed when ultrasonic or Burgener nebulisers were used (
The results indicated that the Ari Mist and 180 kHz ultrasonic nebulisers gave comparable levels of delivery efficiency with between 20 and 30% GFP positive cells detected. The cell viability was higher with the Ari Mist head. Furthermore, this nebuliser is smaller, easier to handle and does not require to be powered to operate. All these reasons contributed to selection of a nebulizer, e.g., Ari Mist nebuliser, as spray head for soluporation and the optimal delivery parameters evaluated for mRNA delivery, e.g, as shown in Table 4.1. This set of parameters was the result of a wide screening and became the starting point for a further study of refined optimisation whereby in addition to volume, distance and length of spray other parameters such as constituents of the delivery solution, cell number and filter plate were finely tuned to further improve mRNA delivery. Table 4.1 shows a list of parameters and the ranges tested including the preferred parameters for delivery of mRNA (e.g., model cargo GFP mRNA) to T-cells. Table 4.1 includes ranges tested and preferred parameters for both the benchtop Flexi (benchtop) and the Midi (scaled-up) systems.
Optimisation of the Steps for Application of Delivery Solution to Cells Atomiser Height
A number of parameters were assessed in order to increase uptake efficiency and expression of mRNA in human primary T cells. The height at which the AriMist atomiser was assessed to observe if an effect on GFP mRNA delivery to T cells existed. 1×106 human primary T cells were seeded per well in a 96-well filter plate (Pall; Supor, 1.2 μm; CAT# 8039). The plate was centrifuged at 300×g for 5 min and the cell monolayer was sprayed with 40 of delivery solution containing 0.57 μl of GFP mRNA. The atomiser height was assessed at 31, 26 and 11 mm above the bottom of the well (a comparison of 26 mm vs 12 mm was assessed in another experiment). Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. Uptake of mRNA by T cells was achieved when the atomiser was placed 31 and 26 mm above the bottom of the well. In some cases, a percentage of the 4 μl delivered did not enter the well. A preferred height of 12 mm above the bottom of the well was chosen (
Volume delivered
A comparison of volumes was undertaken to determine the optimal volume delivered that would allow the greatest uptake of mRNA by T cells. 1×106 human primary T cells were seeded per well in a 96-well filter plate (Pall; Supor, 1.2 μm; CAT# 8039). The plate was centrifuged at 300×g for 5 min and the cell monolayer was sprayed with 4, 1 or 0.5 μl of delivery solution containing 0.57 μg/μl of GFP mRNA. Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. An optimal volume of 1 μl per well was determined (
Previous experiments used a delivery solution that was hypotonic when compared to the cell. An assessment of delivery solutions where the tonicity was altered by the further addition of KCl was conducted. Human primary T cells were seeded at 1×106 per well in a 96-well filter plate (Pall; Supor, 1.2 μm; CAT# 8039). The plate was centrifuged at 300×g for 5 min and the cell monolayer was sprayed with 40 of delivery solution containing 0.57 μg/μl of GFP mRNA. In the first condition, the delivery solution contained 12.5 mM KCl resulting in a solution hypotonic to the cell. The second condition contained 106 mM KCl resulting in a solution isotonic to the cell cytoplasm. Other concentrations between 10mM and 500 mM, e.g., 12.5 mM KCl, 328 and 500 mM KCl, were also tested. At higher tonicity, 328 and 500 mM KCl and GFP expression was demonstrated at a reduced level. Thus, the useful range is from 12.5 to 500 mM, e.g., 50-150 mM, e.g., 100-125 mM, e.g., 100-110 mM, with 106 mM being a preferred concentration of KCI.
Once the cells were sprayed, Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. An optimal concentration of 106 mM KCl, which was isotonic to the cell, was determined (
Due to the gentle nature of the Solupore technology, the cells can be addressed on numerous occasions, without a drop in the cell viability or functionality. An assessment of the preferred number of “hits” (treatments) was undertaken with, e.g., a 1-, 2- and 3-hit strategy.
Human primary T cells were seeded at 1×106 cells per well in a 96-well filter plate (Pall; PES, 1.2 μm). The plate was centrifuged at 300×g for 5 min and the cell monolayer was sprayed with 1 μl of delivery solution containing 0.57 μg/μl of GFP mRNA. Once the cells were sprayed, Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. For the 2-hit strategy the cells were incubated for 2 hours before the spray process was repeated and the 3-hit strategy had a further repeat after a 2 hour incubation. Before each additional hit, and at the end of the 2 hr incubation, the wells containing the cell suspension were sealed using a film (e.g., Parafilm M) and the plate was placed on top of an agitator, e.g., a vortex mixer, and held for 15 s. The cell suspension was then pipette mixed 3 times. The vibration from the vortex and the mixing enabled the orientation of the cells to be “shuffled” prior to the subsequent hits. Cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. The 3-hit strategy appeared to be optimal when looking at uptake, viability and cell yield (
An assessment of the optimal T cell seeding density using the Agilent PCTE plate was undertaken. Human primary T cells were seeded at 1.25, 2.5, 3.5, 5 and 7.5×105 cells per well in a 96-well filter plate (Agilent; PCTE, 0.4 μm). The plate was centrifuged at 350×g for 2 min and the cell monolayer was sprayed with lμ1 of delivery solution containing 0.57 μl/μl of mRNA. Once the cells were sprayed, Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated for 2 hours before the process was repeated. At the end of this spray the cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. The seeding density of 3.5×105 cells was shown to be optimal (
Masking
It was noted previously that a region of negative cells existed around the edge of the well. It is possible that this edge-effect exists due to either (or combinations of): poor spray targeting; increased volume around edge due to meniscus; or ineffective droplet impact at edge; pressure turbulence at the edges. A strategy to overcome the edge-effect would be to produce a seeding mask that would be present during seeding and removed after centrifugation which would prevent cells from being seeded close to the well edge. To test this theory the masks were placed into the PCTE plate wells reducing the diameter of the well from 5.2 to 4 mm. 2.5×105 cells human T cells were seeded within the mask and 3.5×105 unmasked wells as a control. The plate was centrifuged at 350×g for 2 min and the masks were removed before spraying the cells. This meant that cells were seeded only up to about 0.5 mm from the walls of the well. The cells were sprayed with delivery solution containing 0.57 μg/μl of GFP mRNA using a 1-hit strategy. At the end of the process the cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytornetry. The results showed that the sample from the masked wells gave 67.7% uptake but the samples without the mask had 53.1% uptake, suggesting that there is an edge effect and that by having the mask present for seeding negates this (
To examine the correlation between force exerted from the spray and uptake, force sensor analysis was conducted at different heights and pressures to establish a baseline of results. The pressure that drives the air through the atomizer was adjusted from 0.5 to 2 Bar and the force experienced at the bottom of the well was measured using a force sensor. The height was also adjusted to 31, 26 and 11 mm. The results indicated that air pressure was the single largest factor that affects the force exhibited by the spray with a small drop in force at the lower height of 11 mm. With a force of 2.0 bar at 11 mm, the same force is experienced with the larger heights and the normal pressure of 1.65 bar (
Ranges of conditions suitable for delivery of mRNA to non-adherent cells, e.g., T cells such as primary human T cells, are summarized below.
μm
μm
indicates data missing or illegible when filed
The preferred, e.g., optimal, conditions for delivering mRNA to T cells is outlined in Table 4.1.
Table 4.1 Conditions for mRNA Delivery to T Cells Over Time.
per
indicates data missing or illegible when filed
Delivery and viability compared with electroporation—electroporation is a widely used method for vector-free intracellular delivery. Therefore, delivery efficiency and cell viability levels using the delivery method of the current subject matter was compared with electroporation.
When 3 μM of model payload, 10 kDa dextran-Alexa488, was delivered to A549 cells using the current subject matter technology, delivery efficiency was 52.8% (+/−2.7%) compared with 92.9% (+/−0.6%) for electroporation (
For most delivery methods, effective delivery must be balanced with maintenance of cell viability. In order to examine this balance, a transfection score ((transfected cells/total cells)×(viable cells/ total cells)) was used to obtain an aggregate characterisation of cell loss, cell viability and transfection efficiency for the current subject matter delivery technology compared with electroporation. A score of 1.0 would indicate 100% transfection efficiency, 100% cell viability and that no cells were lost during the procedure. The transfection score for the current subject matter technology was 0.33 (+/−0.05) and for electroporation was 0.51 (+/−0.13) with no significant difference between the scores (
A comparison of Solupore and Nucleofection (4D; Lonza) delivery of mRNA to human T cells was undertaken to benchmark the current technology. The amount of mRNA delivered (μg) was matched per cell. For Soluporation, human primary T cells were seeded at 1×106 cells per well in a 96-well filter plate (Pall; PES, 1.2 μm). The plate was centrifuged at 300×g for 5 min and the cell monolayer was sprayed with 1 μl of delivery solution containing 0.57 μg/μl of GFP mRNA. Once the cells were sprayed, Stop solution (50 μl) was applied after a 2 minute incubation and 30 s later normal media (100 μl) was applied. The cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. For Nucleofection, 5×106 human primary T cells were washed in PBS and resuspended in 40 μl P3 buffer containing 2 μg GFP mRNA (Lonza). The cells were then added to the nucleocuvette strip and nucleofected as per instructions. 100 μl media was added to each well and transferred to recovery flask containing 10 mis media. The cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry. GFP mRNA expression levels were 40.3% and 89.3%, respectively (
Diffusion of cargo into cells and resealing of plasma membrane. Having demonstrated the ability of this method to deliver a broad range of cargoes to a range of cells types, the mechanism of cargo uptake into cells and the reversal of the cell permeability was examined. A limitation of other delivery techniques is their dependence on active uptake pathways such as endocytosis which can lead to sequestration of the cargo rendering it unavailable to function in the cell. For example, liposome-mediated delivery involves both clathrin- and caveolar-mediated endocytosis (Cui S, Wang B, Zhao Y, Chen H, Ding H, Zhi D, et al. Transrnernbrane routes of cationic liposome-mediated gene delivery using human throat epidermis cancer cells. Biotechnol Lett. 2014; 36(1):1-7. doi: 10.1007/s10529-013-1325-0. PubMed PMID: 24068499; PubMed Central PMCID: PMCPMC3889874.) while iTOP delivery involves macropinocytosis (D′Astolfo D S, Pagliero R J, Pras A, Karthaus W R, Clevers H, Prasad V, et al. Efficient intracellular delivery of native proteins. Cell. 2015; 161(3):674-90. doi: 10.1016/j.ce11.2015.03.028. PubMed PMID: 25910214.).
During the experiments using Soluporation, immediate uptake of cargo into cells was observed. Using 10 kDa dextran-FITC as a model cargo, within 30 sec of applying the delivery solution, before Stop solution was added, cargo was visible within the cells (
It was noted that the delivery method was very gentle on cells with little if any cell death or damage evident. The method allows the permeabilised plasma membrane to reseal rapidly, hence retaining high levels of cell viability. To examine the rate of recovery of the cell membrane after permeabilization, delivery solution was applied to A549 cells in the absence of cargo. At subsequent time points (0 to 182.5 min), this delivery solution was removed and 50 μl PBS containing propidium iodide (PI) (100 μg/ml) is added. After 2 min incubation, the PI solution was removed and the cells were harvested. PI uptake was analysed by flow cytometry. For basal levels of PI uptake, untreated cells received 50 μl PI in PBS. The results demonstrate that the cells remain permeable to PI for several minutes but reseal over a period of 6 min post treatment (
In order to demonstrate another functional output of T cells following delivery of cargo, gene editing of T cells was assessed using CRISPR/Cas9 RNP delivery.
Equimolar amounts of crisprRNA (a mixture of both GCGTGACTTCCACATGAGCG (SEQ ID NO:3) and GCAGTTGTGTGACACGGAAG (SEQ ID NO:4) crisprRNAs, also equimolar amounts; (Su, S. et al. CRISPR-Cas9 mediated efficient PD-1 disruption on human primary T cells from cancer patients. Sci. Rep. 6, 20070; doi: 10.1038/srep20070 (2016)) and tracrRNA were incubated for 10 min at RT. 5 μg Cas9 (IDT) was then added so that the final molar ratio of Cas9 to guide RNA was 1:3 and incubated for a further 10 min at RT. Cas9 RNPs (in buffer, with a-crystallin (220 μM) and Ethanol (25% v/v)) were delivered to T cells by using the vector-free intracellular delivery method described. Using the vector-free delivery method described herein, RNPs were delivered to 1.5×106 cells per treatment and PD-1 expression was analysed at 72 h post-transfection.
Cell viability. FACS Sample Preparation and Analysis: Cell viability following the vector-free intracellular delivery method, delivery was assessed using 7-AAD viability staining solution (Sigma). Cells were in washed in PBS +1% fetal bovine serum (FACS buffer) followed by incubation with 7-AAD (1:40 for 5-10 min protected from light at room temperature), followed by resuspension in PBS +1% FBS (FACS buffer). PD-1 labelling was carried out using APC-conjugated anti-human CD279 (PD-1) (Biolegend) and processed on the BD Accuri C6 flow cytometcr (Becton Dickinson, USA). Data was analysed using the C6 software. Cell debris was excluded from whole cells using forward and side scatter parameters. Single cells were selected by excluding doublets in the FSC height vs FSC are plot. GFP expression was analyzed on gated viable cells.
Knock-down of immune check point gene expression such as PD-1 expression in T cells following vector-free delivery of CRISPR/Cas9 RNPs
CRISPR/Cas9 RNPs targeting the PDCD1 gene were delivered to T cells using either the vector-free intracellular delivery method described herein or by clectroporation. PD-1 expression was analysed by flow cytometry 72h post-transfection.
Delivery of CRISPR/Cas9 gene editing tools to activated T cells resulted in a 28% reduction in PD-1 expression by the vector-free intracellular delivery method described herein compared with 53% inhibition in electroporated cells (
The proliferative capacity of gene-edited cells was assessed over a 4-day period by observing the formation of T cell aggregates in culture. Following delivery of RNPs, cells were returned to culture. After 4 days, cells were observed using a microscope. Cell aggregation in the vector-free intracellular method-transfected cells was similar to untreated control activated cells indicating that they were not affected by the vector-free intracellular delivery method described. In contrast, the growth rate of electroporated cells was significantly affected as indicated by significantly fewer cell aggregates (
CAR-T: Expression of Chimeric Antigen Receptor (CAR) in Primary T Cells Following mRNA Delivery
mRNA generated from a commercially sourced CD19 CAR plasmid was successfully delivered to human-derived activated T cells. Surface expression of the CAR was detected by flow cytometry with up to 50% of the population positive for CAR expression.
Cell culture. Human peripheral blood mononuclear cells (PBMC) were recovered by centrifugation over a Percoll gradient from Leuko Pak (AllCells Alameda, CA). CD3+ enriched lymphocytes were isolated by magnetically activated cell sorting using CD3 Microbeads (Miltenyi). Cells were cryopreserved in 10% dimethyl sulphoxide (DMSO) and foetal bovine serum (FBS). Following initial thawing from stock aliquots, CD3+ T cells were cultured in human recombinant interleukin-2 (IL-2) with primary and co-stimulatory antibody activation using various protocols (see below) in a humidified tissue culture incubator at 37° C. and 5% CO2.
A CD19 CAR plasmid was sourced commercially (Creative Biolabs, NY, USA) and mRNA generated from the plasmid. The full length of chimeric antigen receptor (CAR) was synthesized and subcloned into lentivirus vector. The insert was confirmed by Sanger sequencing. The structure of CAR vector is illustrated in
CAR mRNA Delivery
4 μg of mRNA (from CD19 CAR plasmid described above) was added to Buffer and Ethanol (27% v/v) also added and delivered to 1.5×106 T cells using technology described herein to 1.5×106. 24 hr later the cells were harvested and analysed for mRNA expression using flow cytometry.
Biotinylated protein L (AcroBiosystems) was reconstituted in phosphate buffered saline (PBS) at 1 mg/ml. For FACS staining, 1×106 cells were harvested and washed three times with ice cold PBS containing 4% bovine serum albumin (BSA) wash buffer. After wash, cells were resuspended in 0.2ml of the wash buffer and incubated with 1 μg of Protein L for 45 minutes at 4° C. Cells were washed a further three times and then incubated in the dark with 10 μl of PE-conjugated streptavidin in 0.2 ml of wash buffer. To assess cell viability following the vector-free delivery method described herein, 7-AAD (Sigma) was used to stain the cells. Briefly, cells were in washed in PBS +1% fetal bovine serum (FACS buffer) followed by incubation with 7-AAD (1:40 for 5-10 min protected from light at room temperature), followed by resuspension in PBS +1% FBS (FACS buffer). Samples were processed on the BD Accuri C6 flow cytometer (Becton Dickinson, USA) and data was analysed using the C6 software. Cell debris was excluded from whole cells using forward and side scatter parameters. Single cells were selected by excluding doublets in the FSC height vs FSC are plot. CAR-T expression was analysed on gated viable cells.
Untransfected cells were used as untreated controls (UT). A shift in fluorescence intensity was observed using the delivery method for treated cells was indicative of CAR expression following mRNA delivery (
In order to demonstrate that the functionality of T cells transfected using Solupore technology is equivalent to or better than cells transfected using electroporation, e.g., with the Neon electroporator, and nucleofection, e.g., using the Lonza 4D nucleofector. Cell membrane protein expression, gene expression, cell proliferation rate, in vitro functionality and in vivo functionality assays were carried out.
The goal of this study was to determine whether expression of cell surface proteins on T cells was affected by the soluporation process and to compare with electroporation and nucleofection.
Method: Activated T cells were seeded at 1.5×106 cells per well of a 96-well filter plate (Acroprep, 1.2 μm Supor membrane; Pall, USA). Media was removed from the wells by centrifugation at 300×g for 5 min. 7 μl of delivery solution (32 mM sucrose, 12 mM potassium chloride, 12 mM ammonium acetate, 5 mM HEPES and 27% ethanol in molecular grade water (all from Sigma-Aldrich)) containing 4 μg GFP mRNA was then sprayed into each well using the vector-free delivery spray instrument. Following delivery, the cells were incubated in this solution for 2 min prior to the addition of 50 μl Stop Solution (0.5× PBS). Thirty seconds later T cell media was added (100 μl) and cells were allowed to recover at 37° C. and 5% CO2 overnight. For electroporation and nucleofection, 5×106 cells and 2.5×106 cells were used respectively per transfection. GFP expression and viability were assessed at 6h and 24h post-delivery.
The expression of cell surface CD4 and CD8 was examined at 6 hr and 24 hr after either nucleofection, electroporation or Soluporation. At 6 hr post-transfection, the percentage of T cells expressing CD4 and CD8 was unchanged compared to untreated control cells for each transfection method. However, at 24 hr, expression was significantly reduced in electroporated cells whereas expression in soluporated cells and nucleofected cells was similar to control untreated cells (
(ii) Global mRNA Expression Analysis
The goal of this study was to obtain a molecular signature of cellular perturbation induced by the soluporation process, and to compare that signature with electroporation and nucleofection. 16 samples were analysed using mRNA microarrays: two donor T cells were taken, samples included an untreated control, neon, nucleofector and Solupore transfected cells with GFP-mRNA, at 6 hr and 24 hr time points.
Method: Activated T cells were seeded at 1.5×106 cells per well of a 96-well filter plate (1.2 μm PES membrane; Pall, USA). Media was removed from the wells by centrifugation at 300×g for 5 mM. 1 μl of delivery solution (32 mM sucrose, 12 mM potassium chloride, 12 mM ammonium acetate, 5 mM HEPES and 27% ethanol in molecular grade water (all from Sigma-Aldrich)) containing 0.2 μg GFP mRNA was then sprayed into each well using the vector-free delivery spray instrument. Following the spray, cells were incubated in this solution for 2 min prior to the addition of 50 μl Stop Solution (0.5× PBS). Thirty seconds later T cell media was added (100 μl). A second spray was carried out 2 hrs after the first. Cells transferred to an incubator at 37° C. and 5% CO2. For electroporation and nucleofection, 5×106 cells and 2.5×106 cells were used respectively per transfection. GFP expression and viability were assessed at 6 h and 24 h post-delivery.
The highest level of gene expression changes occurred in Neon electroporation treatments. However, a drawback of electroporation is reduced viability and functionality of the treated cells post-electroporation. Of the 20,893 mRNAs analysed, Neon electroporation had a combined total of 317 changed over all timepoints (6 hr and 24 hr) and both donors, Soluporc had 32 changed (Tables 5.1 and 5.2) and nucleofector had 24 changed (Tables 5.3 and 5.4;
like transcription factor
indicates data missing or illegible when filed
The data indicate that only a low number (e.g., negligible) of changes in gene expression occur in soluporated cells at 6 hr post transfection.
indicates data missing or illegible when filed
The data indicate that only a low number (e.g., negligible) of changes in gene expression occur in soluporated cells at 24 hr post transfection.
signaling pathway
P
indicates data missing or illegible when filed
The data indicate that only a low number (e.g., negligible) of changes in gene expression occur in nucleofected cells at 6 hr post transfection.
monophosphate kinase 2
signaling pathway
dioxygenase 2
domain containing 7
-like receptor signaling pa ...
regulatory factor 1
signaling pathway
repeat containing 4
receptor, C type 1
kinase C1
STAT signaling pathway
beta 118
guanine nucleotide exhange factor 1
signaling pathway
signaling
indicates data missing or illegible when filed
The data indicate that only a low number (e.g., negligible) of changes in gene expression occur in nucleofected cells at 24 hr post transfection.
(iii) Cell Proliferation Analysis
For therapeutic applications, it is necessary that T cells are able to proliferate following modifications. Therefore, the ability of T cells to proliferate following soluporation, electroporation and nucleofection was examined. The cells capacity to proliferate post-cryopreservation and thaw was also tested.
Method: Activated T cells were seeded at 1.5×106 cells per well of a 96-well filter plate (Acroprep, 1.2 μm Supor membrane; Pall, USA). 10 of delivery solution containing 0.2 μg GFP mRNA was then sprayed into each well. A second spray was carried out 2 hrs later. For electroporation and nucleofection, 5×106 cells and 2.5×106 cells were used per transfection. Cells were transferred to an incubator at 37° C. and 5% CO2. The next day, cells were harvested and counted. Cells were then re-seeded at 0.5×106/ml by adding additional media +IL-2 each day for 7 days. In another experiment, cells were cryopreserved in 10% DMSO and foetal bovine serum 24 hrs post-transfection. Cells were thawed and seeded at 0.5×106/ml on day 0 in Immunocult media +IL-2. Cells were counted and re-seeded by adding additional media each day for 5 days.
T cells were transfected and cells were counted each subsequent day for 7 days. Proliferation rates in soluporated and nucleofected cells were similar to untreated control cells whereas the ability of Neon electroporated cells was reduced compared with control cells (
For therapeutic applications, it is necessary that T cells are able to produce IFNg following modifications. Therefore, the ability of T cells to produce IFNg following soluporation, electroporation and nucleofection was examined. Two different activation methods were examined, phorbol myristate acetate/ionomycin (PMA/I) and Dynabeads. The cells ability to secrete IFN-γ was also tested post-cryopreservation and thaw following soluporation.
Method: Activated T cells were seeded at 1.5×106 cells per well of a 96-well filter plate (Acroprep, 1.2 μm Supor membrane; Pall, USA). 10 of delivery solution containing 0.2 μg GFP mRNA was then sprayed into each well. A second spray was carried out 2 hrs later. For electroporation and nucleofection, 5×106 cells and 2.5×106 cells were used respectively per transfection. Cells were allowed to recover at 37° C. and 5% CO2. The next day, cells were harvested and counted. Cells were then re-seeded at 0.5×106 /ml by adding additional media +IL-2 each day for 7 days, after which the cells were allowed to return to a resting state by monitoring cell size. This was approximately 2 weeks after initial activation. Cells were then re-stimulated with either Dynabeads or a PMA/Ionomycin cocktail for 4 hrs, after which the supernatants were recovered and stored at -20° C. until cytokine analysis. IFN-γ ELISA (Biotechne) were carried out on all samples. In another experiment, Soluporated, nucleofected and electroporated cells were harvested and counted 24 h after transfection. Cells were then re-seeded at 0.5×106/ml by adding additional media +IL-2 each day for 7 days, after which the cells were allowed to return to a resting state by monitoring cell size. This was approximately 2 weeks after initial activation. Cells were then re-stimulated with either Dynabeads or a PMA/Ionomycin cocktail for 4 hrs, after which the supernatants were recovered and stored at −120° C. until cytokine analysis. IFN-y ELISA (Biotechne) were carried out on all samples.
IFNg production was not reduced in T cells following soluporation, nucleofection or electroporation compared with control cells (
(v) In Vivo Engraftment in T Cells Following Delivery of 3 kDa Dextran
In order to determine the effect of Solupore technology on T cell functionality, the capacity of transfected PBMC to induce GvHD in a NSG mouse model was studied. NOD scid gamma mice (NSG mice) is an art-recognized immunodeficient laboratory mouse strain from The Jackson Laboratory.)
If transfected cells were adversely affected by the Solupore delivery technology, their ability to engraft and induce Graft versus Host Disease (GvHD) would be impaired. A comparison with nucleofection was also carried out. It was impractical to include Neon electroporation as a comparator because the high loss of cells in the process would require an unfeasibly high number of cells to be electroporated.
Method: 3 kDa Dextran-Alexa488 was delivered to 20×106 and 5×106 PBMC by soluporation and nucleofection respectively. Soluporation was carried out using the 44.45 mm Stirred Cell system. A monolayer of cells was formed on a 1 μm PCTE hydrophilic membrane (Sterlitech) by applying a pressure of 100 mbar for 15-25 secs until all media was removed. 5 ml of delivery solution containing 3 μM Dextran 3000 was prepared and loaded into the LP100 atomiser. Cells were soluporated and after 1 min and 30 sec, the membrane was gently transferred to a 60-mm cell culture grade petri dish. After 2 mins, 1 ml of stop solution was added to the membrane and left to incubate for 30 seconds, after which time, 4 ml of media was added to the cells. The petri dish was transferred to an incubator at 37° C. with 5% CO2 for 30 mins. For nucleofection, 5×106 cells were used per transfection. Cells were harvested, washed twice in 1× PBS and resuspended according the weight of the mouse i.e. 1×106 per gram. injected intravenously via the tail vein based on weight per mouse (1×106 per gram). Mice were weighed 2-3 times weekly and monitored for the appearance of GvHD-like symptoms. Peripheral blood was collected between 9-12 days post-injection and processed for flow cytometry analysis. Similarly, blood and spleen were collected at the end of the study and prepared for analysis.
PBMC were isolated from three different donors (D119, D120, D121) and cells from each donor were soluporated or nucleofected. There were four groups of NOD scid gamma (NSG) mice, with 5 mice per group, for the study. The groups were: 1. No cells 2. UT 3. Soluporation 4. Nucleofection (4 groups×5 mice p/group×3 donors=60 mice). Cells were injected into the mice on Day 0. Animals were monitored daily and GvHD symptoms were present by Day 14 post injection in all animals that received cells indicating that cells were viable and functional. Blood samples were taken from the mice on Day 14 and analysed by flow cytometry for the presence of human PBMC, as indicated by CD45 expression, and T cell subsets. Results demonstrated that CD45+ cells were present in the untreated groups and soluporated groups at this timepoint, confirming that the cells were viable and functional (
To facilitate and to enhance the exposure of cells (non-adherent cells or adherent cells) to permeableisation solution, the filter membrane is optionally vibrated before or after or during delivery or permutations of these. To assist in the formation of a monolayer of cells on a filter membrane, the membrane can vibrate before or after or during delivery or permutations of these. Vibration of a filter membrane can be carried out using a number of readily available devices, e.g., Piezoelectric Accelerometers such as a Miniature Triaxial DeltaTron® Accelerometers (available from Bruel and Kjaer, www.bksv.com). A number of other suitable vibrating motors are also available from Precision Microdrives; www.precisionmicrodrives.com.)
For example, the vibration may be brought about by an eccentric rotating mass (ERM) system or a linear resonant actuator (LRA) system. By preference, 1, 2 or 3 actuators (LRA) corresponding to the X, Y and Z axis may be attached to the membrane or membrane holder such that the membrane vibrates by mechanical coupling to the actuator.
The advantage of the LRA system is that each axis may be driven independently. Accordingly, complex but controllable vibration patterns may be developed on the membrane. Additionally, identification of mechanical resonance points due to the physical character of the membrane will improve the degree of control that may be exhibited over the membrane. A 3 axes accelerometer device will be mechanically coupled to the filter membrane or holder to feedback the excursions experienced by the membrane. The Accelerometer system may be used to monitor or as a control feedback signal to the vibrational system, generating an error signal between the desired vibrational pattern and the achieved vibrational pattern. The selection of driving vibrational frequencies is made based on the stiffness of the membrane and the size of cells on the membrane. An example vibrational pattern is brought about with sinusoidal signals at 3000 Hz on the x and y axes and no signal on the z axis. The excursions are 1 mm peak to peak and the x and y driving waveforms are coherent with no phase difference between them. Many other patterns are possible including ones that lead to swirling, shaking in the x, y and/or z axes.
The current subject matter generally relates the delivery biological payloads to cells. The delivery of biological payloads to cells can involve the atomization and delivery of a permeabilizing solution onto a monolayer of cells. Current techniques can fall short in a number of areas, which is discussed in more detail below.
Prior to receiving the payload, the cells can be submersed or suspended within a culture medium. To achieve effective payload uptake, it can be beneficial to remove the culture medium so that cells can be exposed to the permeabilizing solution, and to organize the cells in a monolayer conformation. With certain current techniques, the medium is removed by centrifugation. Although this technique can be effective at removing the medium, it typically does not result in the formation of a uniform monolayer of cells.
In order to ensure an appropriate distribution of the permeabilizing solution on the monolayer of cells, the cells can be aligned under a solution atomizer or nebulizer. With current techniques, cells are generally aligned under the atomizer using a manual system, which is subject to operator variability. The atomizer/nebulizer can be used to dispense the permeabilizing solution onto the monolayer of cells. However, certain atomizers arc designed to dispense volumes of solution on the order of magnitude of milliliters, while dispensation volumes on the order of microliters can be preferable, or even required. Additionally, the transfection protocol for payload delivery can involve several time critical steps. Currently, handling of fluids is generally controlled manually, and it is therefore intrinsically variable.
Because of these shortcomings, the data generated can be inherently inconsistent. The lack of reproducibility of the data can hamper further development of the payload delivery process. In order to address the aforementioned issues, some aspects of the current subject matter provides a delivery system that enables greater consistency in the delivery process, and higher efficiency of delivery, while maintaining cell health.
Example Delivery System
As an example, in some embodiments, the differential pressure applicator 8806 can be, or can include, a nozzle valve assembly, e.g., the nozzle valve assembly 9310, described below with regard to
The delivery system 8800 can also include a control system 8814, an actuation system 8816, a support frame 8818, and a sensing and management system 8820. In some embodiments, the differential pressure applicator 8806, delivery solution applicator 8808, stop solution applicator 8810, and/or the culture medium applicator 8812 can be coupled to the support frame 8818. The actuation system 8816 can coupled to the support frame 8818, the housing 8802, and/or the plate 8804, and can be configured to move the support frame 8818, the housing 8802, and/or the plate 8804. As another example, the actuation system 8816 can be coupled to, and configured to move, the differential pressure applicator 8806, delivery solution applicator 8808, stop solution applicator 8810, and/or the culture medium applicator 8812. For example, the support frame 8818 can be, or can include, the fluidic head module 9308, described below with regard to
The sensing and management system 8820 can include sensors and/or thermal management systems. As an example, the sensors and/or thermal management system can be coupled to the differential pressure applicator 8806, delivery solution applicator 8808, stop solution applicator 8810, and/or the culture medium applicator 8812, and can be configured to measure and/or control pressures, temperatures, positions, and flow rates.
The control system 8814 can include at least one data processor and can be electrically coupled to the actuation system 8816 and the sensing and management system 8820. The control system can be configured to control the actuation system 8816, as well as the sensing and management system 8820. As an example, the control system 8814 can be, or can include, the control system 9306 described below with regard to
Example Vacuum Pressure System
The delivery system can address the following areas of variability related delivering a payload to cells: monolayer formation; atomization; automation of the payload delivery; and temperature control of the solutions and the culture container.
In order to improve the consistency of the data and the delivery efficiency of payload delivery, the system removes certain known sources of variability from the process. The system can address: removal of media and creation of a monolayer of cells using a vacuum; atomization of the permeabilizing solution to produce monodispersed droplets; fluidic control of the solutions to enable automation; temperature control of the solution; mounting of a spray head and a temperature reservoir; automation and software design; enclosure for the instrument; and temperature control of a base plate.
The needle emitters 9002 can function to deliver a culture medium, which can contain cells, to wells of the filter plate 9014. The base plate 9016 can have vacuum couplings 9020 extending from a bottom surface thereof. The vacuum couplings 9020 can generally be in the form of cylindrical tubes, and can allow vacuum pressure to be applied to corresponding wells of the filter plate 9014. Vacuum pressure can be routed through ports 9024a of the manifold 9024 to each valve 9011, and to the vacuum couplings 9020. The atomizer 9004 can atomize a pemieabilizing solution and deliver it to cells within a well of the filter plate 9014. Systems, devices, and methods related to the delivery a peiuieabilizing solution onto a monolayer of cells are discussed in more detail below.
As shown in
Referring to
The base plate 9016 can include a first recessed region 9028 where the filter plate 9014 can be received, or seated, as well as secondary recessed regions 9030 that can receive gaskets 9026. Each of the secondary recessed regions can have openings 9030b or passages that can couple with corresponding vacuum couplings 9020.
The filter plate 9014 can have wells that have active openings 9014b, in addition to having wells that have inactive openings 9014c. The active openings 9014b can be positioned over, and fluidly coupled to, openings 9030b in the base plate 9016. In other words, certain wells of the filter plate 9014 can be active, while other wells of the filter plate 9014 can be inactive.
The gaskets 9026 can have bores 9026b that can align with active openings 9014b of wells in the filter plate 9014 and with the openings 9030b in the base plate 9016. The gaskets 9026 can function to form seals between the base plate 9016 and the filter plate 9014, thereby isolating each active opening 9014b from other active openings 9014b, as well as from inactive openings 9014c, while allowing fluid communication between the active openings 9014b of the wells and corresponding vacuum couplings 9020.
In some embodiments, all of the wells of the filter plate 9014 can be coupled to different valves 9011, and to a manifold, such that all of the wells can be active.
Removal of Media and Creation of a Cell Monolayer Using a Vacuum
The vacuum manifold system 9006 can remove a culture medium from between 1 and 12 wells of the filter plate 9014, with a total of 6 wells being addressable at a one time.
As described above, vacuum pressure can be routed through a manifold 9024 to each valve 9011, and to the vacuum couplings 9020.
The vacuum manifold system 9006 can be used to enable formation of a monolayer of suspension cells. As described above, needle emitters 9002 can deliver a culture medium, which can contain cells, to wells of the filter plate 9014. Vacuum pressure can be applied to the 8-channel manifold via the vacuum line. The valves 9011 can be opened or closed individually. Therefore, access to each active well can be controlled individually. When the valves 9011 are open, the applied vacuum pressure can be sufficient for effective removal of the culture medium in which the cells are suspended, without causing shear force that can lead to damage. The extracted medium can travel through the tubing 9034 and the valves 9011, through the manifold 9024, and out of the port 9024a where the vacuum line is attached. In this way, a cell monolayer can be formed and cell viability can be maintained. The formation of the cell monolayer can be achieved without damaging cells.
The vacuum manifold system 9006 has been built and tested. During testing a culture medium having cells was added to wells of a 96-well filter plate 9014. Vacuum pressure was applied via the manifold 9024. Vacuum pressure ranging from 10 bar to 100 mbar was applied to individual wells by opening the well's associated valve 9011.
At higher vacuum pressures, between −100 mBar and −75 mBar, the culture medium was removed far enough away from the well that when the filter plate 9014 was removed, the culture medium did not “wick” back into the well.
At lower pressures, between −50 to −10 mBar, the media stayed close enough to the well that when the filter plate 9014 was removed from the vacuum manifold assembly 9008, some of the medium “wicked” back in to the well. The amount of liquid that wicked back into the well was between approximately −5-10 μI. This may not be a problem when the vacuum manifold assembly 9008 is part of the precision rig system 9000 as the well will be sprayed and have the culture medium replaced before the filter plate 9014 is removed from the manifold.
In some embodiments, filter paper, or other materials, can be used to prevent wicking. For example, filter paper can be placed between the gaskets 9026 and the base plate 9016 to prevent wicking of the media back into the well.
At pressures, as low as −10 mBar the culture medium was removed at a sedate, controlled rate which was gentler on the cells. This occurred both in presence and absence of cells. This can lead to better viability and recoverability of cells from the wells.
During testing, pulsing the valves 9011 on and off did not appear to aid in the removal of the culture medium.
Centrifugation was also investigated as a method of forming a cell monolayer. However, this was found to be ineffective as it formed an uneven layer of cells.
As shown in
Comparable results of mRNA uptake using vacuum and spin methods were achieved, even at −10 mBar. The GFP MFI was found to be greater in samples prepared by the vacuum vs spin (300,000 vs 50,000 units). This indicates that more mRNA got into the positive cells.
The time needed to extract the culture medium from the wells is estimated to be between approximately 3 s and 20 s. However, the amount of time that it takes to remove the culture medium from the wells can be dependent on the amount of vacuum pressure that is applied. More work can be done to test the length of time required to remove the media at the lower vacuum pressures.
In some implementations, it is possible to be able to evacuate all wells at the same time at a lower pressure to remove residual media from the spouts (no plate on the manifold).
The vacuum manifold system 9006 allows vacuum pressure to be applied to individual wells of a filter plate 9014. By applying a vacuum pressure to individual wells on a filter plate 9014, greater precision control of the vacuum pressure, and greater consistency of the vacuum pressure applied to each well, can be achieved. Existing vacuum manifolds apply a vacuum to an entire 96-well filter plate. During testing, lower vacuum pressures were effective in removal of the culture medium and creation of an even monolayer of cells within the well.
Example Positive Pressure System
The positive pressure delivery system can address the following areas of variability related delivering a payload to cells: monolayer formation; atomization; automation of the payload delivery; and temperature control of the solutions and the culture container.
In order to improve the consistency of the data and the delivery efficiency of payload delivery, the system removes certain known sources of variability from the process. The system can address: removal of culture medium and creation of a monolayer of cells using a positive pressure; atomization of the penneabilizing solution to produce monodispersed droplets; fluidic control of the solutions to enable automation; temperature control of the solution; mounting of a emitters, atomizers, nebulizers, and a temperature reservoir; automation and software design; enclosure for the instrument; and temperature control of a base plate configured to retain a well plate.
The manifold assembly 9305 can include a base 9312, also referred to as a plate holder, that can extend from a housing 9314 of the manifold assembly 9305. The base 9312 can be configured to receive filter plate 9316. As shown in the illustrated example, the filter plate 9316 can be a 96-well filter plate.
The mounting array 9302 can include fluidic head modules 9308 having needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310 attached thereto. The needle emitters 9303 can be configured to deliver a culture medium, which can contain cells, and a stop solution to wells of the filter plate 9316. The nebulizers 9304 can be configured to atomize a permeabilizing solution and deliver it to cells within wells of the filter plate 9316. The positive pressure nozzle assembly 9310 can be configured to apply a positive pressure to wells of the well filter plate 9316 to remove a liquid portion of the culture medium from the well, thereby creating a monolayer of cells. Systems, devices, and methods related to the delivery a penneabilizing solution onto a monolayer of cells are discussed in more detail below.
In some embodiments, the positive pressure system 9300 can include a guide rail 9318. In the illustrated example, the filter plate 9316 can be held stationary, and a position of the mounting array 9302 can be adjusted relative to the position of the filter plate 9316. For example, the mounting array 9302 can be coupled to a guide rail 9318, which can allow the mounting array 9302 to be translated along an axis X2 defined by the guide rail 9318. For example, an actuator 9319 can move the mounting array 9302 along the guide rail 9318. The guide rail 9318 can also be moved along an axis Y2, which can be perpendicular to the axis X2. The actuator 9319 can also move the mounting array 9302 along the axis Y2. Therefore, the mounting array 9302, including the needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310 can be selectively positioned above wells of the filter plate 9316 when the filter plate 9316 is positioned within the housing 9314.
As an example, a user can insert the filter plate 9316 into the base 9312, which can then be positioned within the housing 9314. The filter plate 9316 can be held stationary after it is received within the housing 9314. The filter plate 9316 can be selectively addressed by needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310 coupled to fluidic head modules 9308 of the mounting array 9302. In the illustrated example, the mounting array 9302 includes six fluidic head modules 9308. Two fluidic head modules 9308 include needle emitters 9303, three fluidic head modules 9308 include nebulizers 9304, and one fluidic head module 9308 includes a positive pressure nozzle assembly 9310. The mounting array 9302 can be moved along the axes X2, Y2, such that each of the fluidic head modules 9308, including the needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310, can address any location on the filter plate 9316.
In some embodiments, each of the individual fluidic head modules 9308 can have the capability to move up and down parallel to an axis Z2, which allows for independent actuation of the fluidic head modules 9308. In some embodiments, movement of the fluidic head modules 9308 and actuation of needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310, are controlled independently. The movement of one or more of the fluidic head modules 9308, and actuation of needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310 attached thereto, can occur contemporaneously. In some implementations, the fluidic head modules 9308 activate the needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310 when they move toward the filter plate 9316. The fluidic head modules 9308 can accommodate a variety of fluid dispensing assemblies, including but not limited to, needle assemblies, Ari Mist nebulizers, and positive pressure nozzle assemblies, as shown in
The actuation and control system (ACS) 9306 can include at least one data processor, and can control movement of the mounting array 9302 and/or the fluidic head modules 9308. The ACS 9306 can also control actuation of the needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310 attached to the fluidic head modules 9308. For example, the ACS 9306 can include software, having instructions that can be interpreted by the data processor of the ACS 9306. The data processor can receive the instructions, process the instructions, and execute the instructions. For example, the data processor can deliver control signals to actuators and/or motors of the ACS 9306 to adjust a position of the mounting array 9302, and/or to actuate needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310.
Example Fluidic Head Module
As described above, the fluidic head modules 9308 provide mounting points for various fluidic dispensing assemblies (e.g., the needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310) such that they can be coupled to the mounting array 9302. The fluidic head modules 9308 also provide actuation along the axis Z2 such that the dispensing assemblies can be selectively actuated.
The fluidic head module 9308 can include a shaft 9360 that extends between the base plate 9352 and the upper mounting element 9356. The shaft 9360 can extend through an opening in the lower mounting element 9358. A guide 9362 such as, e.g., a ball spline, can be mounted on the shaft 9360 and coupled to the lower mounting element 9358. The guide 9362 facilitates vertical motion of the fluidic dispensing assemblies (e.g. the needle emitters 9303, nebulizers 9304, and/or positive pressure nozzle assemblies 9310) along axis Z2. For example, a pneumatic actuator 9364 positioned between the upper and lower mounting elements 9356, 9358 can drive the lower mounting element 9358 up and down along the shaft 9360. The pneumatic actuator 9364 can drive associated pneumatic fittings as well as two proximity sensors. For example, the sensors can be embedded in a wall of the cylinders.
Removal of Media and Creation of a Cell Monolayer Using Positive Pressure
As described above, positive pressure nozzles can be configured to apply a positive pressure to wells of a well filter plate to remove a culture medium and create a monolayer of cells.
As shown in
As shown in
In some embodiments, a positive pressure nozzle assembly can include a valve positioned along its length. The valve can function as a manual control to control a pressure of air delivered to a well of a filter plate.
Atomization of the Delivery Solution to Produce Monodispersed Droplets
There are a number of different ways in which a pet leabilizing solution can be delivered onto a monolayer of cells. For example, the permeabilizing solution can be atomized using ultrasonication or it can be nebulized using a nebulizer.
Both ultrasonication and nebulization were tested as delivery methods. A total of 4 different spray heads were tested.
The following parameters were assessed for each spray head: Air pressure, flow rate, distance, volume delivered, cell number, time of spray, frequency of ultrasonic probe, and power of ultrasonic probe.
The effect on the character of the spray was assessed using high-speed camera recording. The force experienced by the cells was determined by force sensor analysis. The volume delivered into the well was assessed using a colorimetric assay.
Ultrasonication tests were perfoiuied at 60 kHz, 130 kHz, and 180 kHz. Liquid can be driven to an ultrasonic nozzle by a pumping system, and it can be atomized into a fine mist spray using high frequency sound vibrations.
Piezoelectric transducers were used to electrical input into mechanical energy in the form of vibrations, which created capillary waves in the liquid when introduced into the nozzle, and resulted in atomization of the liquid. Each ultrasonic probe worked at a given resonant frequency. The operating frequency can determine the size of the liquid droplets generated. The size of the droplets can also be affected to a lesser extent by the power at which the ultrasonic probe is operated. An ancillary air stream can be used to help control and shape the spray.
Nebulization tests were performed using an Ari Mist nebulizer 9304 (
The ultrasonic emitter operating at 180 kHz proved to be more effective compared to the 130 kHz, 60 kHz ultrasonic heads and the Ari Mist nebuliser in delivering payloads to T-cells.
The results indicate that the ultrasonic spray emitter generates a monodispersed spray which results in even deposition of the delivery solution and payload onto cells. Additionally reducing the volume delivered and reducing the ethanol concentration improved delivery efficiency with the ultrasonic spray head.
Enclosed Atomization
During delivery of a solution using e.g., an atomizer, nebulizer, and/or ultrasonic emitter, a fine aerosol is generated. In some cases, the fine aerosol may contaminate adjacent wells of a multi-well filter plate. In some embodiments, a distal end portion of an atomizer, nebulizer, and/or ultrasonic emitter can be enclosed, which may prevent contamination of adjacent wells of the filter plate.
Three rig platforms were built: rig 1 (R1), rig 3 (R3) and rig 4 (R4) (
As illustrated in
As illustrated in
As illustrated in
Below is a detailed description of the Rig features which enable fine control of the spray parameters.
In some embodiments (e.g., R1 and R4), fluidic control of the delivery solution containing the payload can be achieved using the Elveflow pinch valve. The fluidic control can be achieved by a fluid control system that can apply a constant pressure to an Elveflow fluidic reservoir to drive the fluid through a pinch valve 9808. A volume of fluid that can be dispensed can be controlled by at least: an amount of pressure applied; a length of time the valve 9808 is open, and/or a diameter of the tubing used. The valve 9808 can be activated by a metal—oxide—semiconductor field-effect transistor (MOS FET) which can be controlled by a microprocessor.
The Elveflow-Pinch valve 9808 described above had several limitations. For example, re-calibration of the R1 and R4 was required every time the system was re-loaded. There was poor accuracy and precision in dispensing volumes lower than 50. For low volumes (<50) the relative standard deviation was approximately 9% over repeated dispenses (10). To address the observed limitations, a R3 was developed. As described above, R3 includes the micro-valve 9368 rather than the pinch valve 9808. Fluidic control of the delivery solution containing the payload can be achieved using the micro valve 9368. R3, which uses the micro valve 9368 had greater accuracy and precision when delivering volumes in the range of 1 μl to 100 μl.
Fluidic control of air delivered to the nebulizers/atomizers can be achieved using a solenoid valve. In some embodiments, electronics can be used to control actuation of the nebulizers/atomizers. To enable electronically controlled spray actuation, a system was designed using a microprocessor based development board to allow easy development of time controlled sequences. The development board used the microprocessor PIC16F1619. The spray actuation time and fluid delivery time can be manipulated through the development board's interface software. The microprocessor development board enables pulsing of the nebulizer/atomizer spray. This system was then upgraded to include the high speed and repeatable PLC (programmable logic controller) technology to better align with industry standards and to serve as proof of concept for the automated delivery technology (which is based on ultra-high-speed PLC technology). The Rig controller consisted of a PLC with a Gyger controller and a program which facilitates communication between the two pieces of hardware. There is operator interaction to the hardware via a momentary push button.
The Ari Mist nebulizer 9304 parallel path design inherently produces a spray which is off center from a tip of nebulizer 9304. Using a custom spray head holder equipped with a goniometer, the alignment of the spray head can be adjusted.
Several methods for delivering a solution using an enclosed emitter were tested. The results of GFP uptake using an enclosed emitter were compared to the results of GFP uptake using an unenclosed emitter.
Method 1: Using a collar to enclose the emitter
Method 1A: The Collar Forms a Seal with the Well Plate.
At a distance of 26 mm from a tip of the spray head 9504 to a base of the well 9516a, the collar 9502 mated with the top of the well 9516a of the filter plate 9516 and formed a seal. CD3+ T-cells, 1.5×106, were seeded in the filter plate 9516 and centrifuged for 5 min at 350×g to remove the culture medium. A delivery solution (4 μl) containing GFP mRNA was sprayed onto the cells and incubated for 2 min. Following the 2 min incubation 50 μl of a stop solution was added and incubated for 30 s. Finally, 100 μl culture medium was added.
Method 1B: Providing a 1 mm Gap Between the Collar and the Filter Plate
The collar 9502 was installed onto the spray head 9504, and the tip of the spray head 9504 was positioned a distance of 27 mm from the base of the well 9516a. Therefore, the collar was held 1 mm above the upper surface of the filter plate 9516. Note: a single hit protocol (e.g., single exposure to delivery solution and stop solution) was followed for the enclosing experiments.
Method 1: Results
The tests corresponding to method 1B, where there was a 1 mm gap between the collar 9502 and the upper surface of the filter plate 9516, shows that the collar 9502 had no impact on GFP uptake. The results highlighted comparable data between the wells with and without the collar 9502 in this set-up. Viability of the T-cells was unaffected using the enclosing collar in both set-ups.
Method 1: Conclusions
The result indicate that the collar 9502 does not affect the viability of T-cells. The collar 9502 does affect the spray, to varying degrees. This variance may be attributed to the degree to which the system is scaled. Scaling the system (e.g., method 1A) led to the formation of a local pressure maxima which inhibited the spray. Regarding method 1B, providing a gap between the collar 9502 and the upper surface of the filter plate 9516 provided an outlet for the pressure. The gap allowed for expansion of the air within the well, and permitted correct actuation of the spray. Therefore, a collar can be used to enclose the spray provided it pen iits expansion space for the air to expand during the spray process.
Method 2: Use of X-pierce film to enclose the spray.
Rather than enclosing a spray head using a collar, an X-pierce film (Sigma Aldrich, Catalog No. Z722529) was used to enclose the spray. The use of an X-pierce film to enclose the spray head may have benefits over the use of a collar (e.g., collar 9502) for enclosing the spray but avoiding the follnation of a seal which can inhibit the spray.
Method 2: Results
The x-pierce film can be used to enclose the spray and avoid cross contamination between wells without reducing efficiency (GFP uptake) or cell viability.
Fluidic Control of the Solutions to Enable Automation
In some embodiments, the precision rig can provide an automated engineering solution for the payload delivery process. To enable this, fine fluidic control of the delivery solution, cold stop solution and culture medium can be used.
The fluidic control can be achieved by fluid control system that can apply a constant pressure to the system to drive the fluid through a pinch valve or micro valve. A volume of fluid that can be dispensed can be controlled by: an amount of pressure applied; a length of time the valve is open; and/or a diameter of the tubing used.
The valve can be activated by a metal—oxide—semiconductor field-effect transistor (MOS FET) which can be controlled by a microprocessor.
The fluid control system can allow fluid volumes in the range of 2-10 μl to be delivered using the fine fluidic control. Therefore, the precision rig system 9000 can control the delivery of metered units of volume in the range of 2-10 μl. In some implementations, other volumes are possible.
Temperature Control of the Solutions (Temperature Reservoirs).
In some embodiments, a fluid temperature control system can be implemented to control the temperature of the delivery solution, stop solution, and culture medium. The fluid temperature control system can include a heating system and a cooling system.
In practice, the delivery solution and the stop solution can be held at approximately 4° C., and the culture medium can be held between approximately 20° C. and 37° C.
Mounting of the Spray Heads and Temperature Reservoirs.
The needle emitters 9002 and the atomizer 9004 can be mounted in a support.
In the illustrated embodiment, a collar 11514 can be attached to the atomizer 11504 and the collar slots in the same head holder at the same height and concentrically to the other two heads.
Similar design templates to those shown in
The designs of the mounting assemblies 11300, 11500, and 11600 enables the precision rig system to perform as a platform for optimization of the delivery process. For example, 4 different spray heads can be accommodated.
Automation and Software Design
The precision rig system 9000, and/or the positive pressure system 9300 can include software program and user interface that can enable automation of the delivery process steps. For example, the software can be designed to control the translational stage 9010 and valves 9011. As another example, the software program can be configured to control movement of the mounting array 9302. A user interface can enable the critical parameters to be entered. A sequence of functional units can be selected by the user.
A system was designed which had the capability of ensuring repeatability of experiments but can also provide the flexibility to adjust experimental specific parameters. Such parameters can include the number of wells one wants to address or the volume which is dispensed into a well. In order to achieve this synchronization, a traverse mechanism (e.g., the actuator 9319) is included, which can be software controlled to position its carriage within a 200 mm location for a required period of time. The carriage includes 6 positions and each of these positions arc coupled to an individually controlled high precision fluid escapement chamber. It is possible to move each position under a selection of dispensing locations (e.g., Payload, Culture Medium and Stop Solution stations). A device specific software platform can be included. The software platform can include: 1) a graphical user interface which enables the user to design an experiment; and 2) local control via a controller (e.g., programmable logic controller (PLC)), for example an Omron PLC.
In some implementations, a system can address ninety six positions within a filter plate substrate. This system can be faster, have multiple traverse mechanism and a user friendly HMI (human machine interface). The HMI can provide the operator with additional automated utilities such as automatic system purging or a touch screen driven calibration sequence. This system can operate as a standalone solution yet still maintained the link to the experimental designer for designing experiment. More aspects of the experiment can be adjusted from well to well, which means the potential permutations greatly increases. For example fluid can be dispense to a number of wells and then the applied pressure to the fluid delivery system for the next section of the experiment can be automatically adjusted. This example system has the capability of recording analytics from the experiments for further offline analysis.
In some implementation, the iteration of operation of the delivery solution applicator, incubation for the first incubation period, operation of the stop solution applicator, and incubation for the second incubation period for a predetermined number of iterations can be performed.
One or more aspects or features of the subject matter described herein can be realized in digital electronic circuitry, integrated circuitry, specially designed application specific integrated circuits (ASICs), field programmable gate arrays (FPGAs) computer hardware, firmware, software, and/or combinations thereof. These various aspects or features can include implementation in one or more computer programs that are executable and/or interpretable on a programmable system including at least one programmable processor, which can be special or general purpose, coupled to receive data and instructions from, and to transmit data and instructions to, a storage system, at least one input device, and at least one output device. The programmable system or computing system may include clients and servers. A client and server are generally remote from each other and typically interact through a communication network. The relationship of client and server arises by virtue of computer programs running on the respective computers and having a client-server relationship to each other.
These computer programs, which can also be referred to as programs, software, software applications, applications, components, or code, include machine instructions for a programmable processor, and can be implemented in a high-level procedural language, an object-oriented programming language, a functional programming language, a logical programming language, and/or in assembly/machine language. As used herein, the term “machine-readable medium” refers to any computer program product, apparatus and/or device, such as for example magnetic discs, optical disks, memory, and Programmable Logic Devices (PLDs), used to provide machine instructions and/or data to a programmable processor, including a machine-readable medium that receives machine instructions as a machine-readable signal. The term “machine-readable signal” refers to any signal used to provide machine instructions and/or data to a programmable processor. The machine-readable medium can store such machine instructions non-transitorily, such as for example as would a non-transient solid-state memory or a magnetic hard drive or any equivalent storage medium. The machine-readable medium can alternatively or additionally store such machine instructions in a transient manner, such as for example as would a processor cache or other random access memory associated with one or more physical processor cores.
To provide for interaction with a user, one or more aspects or features of the subject matter described herein can be implemented on a computer having a display device, such as for example a cathode ray tube (CRT) or a liquid crystal display (LCD) or a light emitting diode (LED) monitor for displaying information to the user and a keyboard and a pointing device, such as for example a mouse or a trackball, by which the user may provide input to the computer. Other kinds of devices can be used to provide for interaction with a user as well. For example, feedback provided to the user can be any form of sensory feedback, such as for example visual feedback, auditory feedback, or tactile feedback; and input from the user may be received in any form, including, but not limited to, acoustic, speech, or tactile input. Other possible input devices include, but are not limited to, touch screens or other touch-sensitive devices such as single or multi-point resistive or capacitive trackpads, voice recognition hardware and software, optical scanners, optical pointers, digital image capture devices and associated interpretation software, and the like.
Enclosure for the Instrument
The precision rig system 9000, and/or the positive pressure system 9300 can be retained within an enclosure to maintain stable ambient conditions. The enclosure can be customized base on parameters to affect the design of the enclosure
Temperature and Control of the Base Plate
In some embodiments, a temperature control system can be implemented to control the temperature of the base plate 9016. For example, cartridge heaters can be installed at various locations on the base plate 9016 of the vacuum manifold assembly 9008. A thermodynamic analysis can be conducted to examine heat transfer from the cartridge heaters to the well filter plate 9014. Temperature ranging experiments can be performed to investigate the effect of temperature on payload delivery.
Although a few variations have been described above, other modifications are possible. For example, the filter plate can include any number of wells, and need not be a 96-well filter plate. Additionally, the system can include any number of valves that can control vacuum pressure to any number of active wells. As another example, the system can include one or more needle emitters, atomizers, and or nebulizers, each of which can be independently mounted and controlled.
The current subject matter provides many technical advantages. In general, the current subject matter provides a delivery system that enables greater consistency in the delivery process, and higher efficiency of delivery, while maintaining cell health.
The delivery system allows for vacuum pressure to be applied to individual wells of a filter plate to remove a culture medium, thereby creating a monolayer of cells. By applying a vacuum pressure to individual wells on a filter plate, greater precision, control of the vacuum pressure, and consistency of the vacuum pressure applied to each well, can be achieved.
The delivery system allows for dispensation of permeabilizing solution in volumes on the order of microliters. Microliter dispensation volumes allow for greater control over cell exposure to the solution, which can increase overall cell viability by reducing excessive exposure to the peiuieabilizing solution. Moreover, the system can be automated which minimizes error, and increases precision.
The system allows for control the temperature of the delivery solution, stop solution, and culture medium. Therefore, each solution can be maintained at an optimum temperature to increase efficiency of payload delivery as well as cell viability. The temperature of the base plate can also be controlled. This allows for temperature optimization to maximize efficiency of payload delivery.
The needle emitters and atomizer and/or nebulizer can be coupled to a mounting assembly that can accommodate various atomizer/nebulizer heights, in the range 15-31 mm from a tip of the emitter to a base of a well of a filter plate, while maintaining a consistent needle emitter height. This allows
The system can include hardware, one or more software programs, and a user interface, that can enable automation of the delivery process steps. The software can be designed to control the translational stage and valves. A user interface can allow for critical parameters, such as to be entered. A sequence of functional units can be selected by the user. This is beneficial because
The enclosure can function to maintain stable ambient conditions.
Additional Example Delivery System Aspects
Scaling the delivery process involved designing a system to enable optimization, determining a method for formation of a cell monolayer at a larger scale, and optimizing atomisation to enable intracellular delivery of mRNA to T-cells.
Optimization work to date has achieved >50% efficiency of mRNA delivery to T-cells with >60% cell viability and cell recovery of up to 80%.
A system was designed and constructed to facilitate scaling of the delivery process. The system is based around the commercially available product, Amicon Stirred cell, pressure-based sample concentration unit (50 ml and 200 ml size; catalogue UFSC05001 and UFSC20001, respectively).
The stirred cell system 9700 can include a cap 9702, a body 9704, a membrane holder 9706, and a base 9708. A stir bar 9710 can be positioned within the body 9704. The cap 9702 can be configured to couple to the body 9704 at a first end of the body 9704. A sealing element 9712 (e.g., a gasket) can be positioned between the cap 9702 and the first end of the body 9704 to form a seal between cap 9702 and the first end of the body 9704. The membrane holder 9706 can receive a membrane 9714, and can be positioned adjacent to a second end of the body 9704 such that a coupling element 9716 of the membrane holder 9706 extends through an opening 9718 in the second end of the body 9704. The second end of the body 9704 can be coupled to the base 9708, and a sealing element 9720 (e.g., an o-ring) can be positioned therebetween to form a seal. A pressure inlet tubing assembly 9722 can be coupled to cap 9702 such that a pressurized gas can be delivered to the body a chamber formed by the cap 9702, the body 9704 and the base 9708. A filtrate tubing assembly 9724 can be coupled to the coupling element 9716 of the membrane holder 9706 such that fluid can be drained from the chamber upon application of pressure.
In operation, a culture medium containing cells can be delivered to the chamber, and the cap 9702 can be coupled to the body 9704. The pressure inlet tubing assembly 9722 can be coupled to the cap 9702, and positive pressure can be applied to the chamber via the inlet tubing assembly 9722. In some embodiments, the pressure can be in the range of 50-1000 mbar, and the pressure can be applied for 10-60 seconds. Accordingly, upon application of positive pressure, the culture medium can be forced through the membrane 9714 and out of the chamber via the coupling element 9716 and the filtrate tubing assembly 9724. With the culture medium evacuated, a monolayer of cells can remain on the membrane 9714. Accordingly, the stirred cell system 9700 can be used to foini the cell monolayer onto a filter membrane placed on the membrane holder of the stirred cell. With the monolayer formed, a nebulizer (e.g., the LB-100 from Burgener Research), can be used to atomize the delivery solution onto the cells sitting on the filter membrane.
The stirred cell system 9700, shown in
To address these limitations with of membrane holder 9706, a membrane holder 9906, shown in
In order prevent accumulation of cells near the holes, and to generate a more even distribution of cells on a membrane, a membrane holder can include holes similar to holes 9906a, but can also include concentric channels that can facilitate radial flow between the holes.
The membrane holder 10006 was assessed using dynabeads.
In some embodiments, a membrane holder can include holes foil ied within concentric channels.
To enable atomisation of the delivery solution using a LB-100 spray head, R4 was built.
The nebulizer assembly 9801 can include a nebulizer 9804 (e.g., the LB-100 spray head), a coupling element 9806 (e.g., an IDEX connection) configured to facilitate delivering air and liquid (e.g., the permeabilizing solution) to the nebulizer 9804, a solution reservoir 9810 (e.g., an Elveflow sample reservoir) configured to provide the penneabilizing solution to the nebulizer 9804, and a pinch valve 9808 configured to control delivery of the pen-neabilizing solution to the nebulizer 9804. The mounting system 9802 can include a valve and reservoir mount 9812, a spray head mount 9814, and a nebulizer retaining collar 9816 to accommodate the nebulizer 9804. The nebulizer assembly 9801 can be coupled to the mounting system 9082, as illustrated in
Additional Example Approaches to Formation of a Cell Monolayer
Two approaches to creating a cell monolayer are described. In both methods, the stirred cell unit was assembled as demonstrated in
The monolayer can be created by applying vacuum pressure to the base of the stirred cell. In this method, −50 to −1000 mbar were applied to the chamber for 10-60 seconds or until the filter membrane appeared dry by eye.
Alternatively the monolayer was formed by applying a positive pressure through the tubing connection on the lid of the stirred cell. Pressure was applied for a set time (10-60 s) or until the filter membrane appeared dry by eye. In some case a lower pressure was used to drive >90% of the culture medium through the filter and then the pressure was gently increased for 10-15 seconds at the end to achieve complete removal of the culture medium. To form the monolayer and completely remove cell culture medium a pressure between 100-200 mbar was applied.
The actual specific pressure and time varied depending on cell concentration, membrane type, pore size and type of membrane holder. For example, with the original unmodified membrane holder, 50-100×106 T-cells were used to form a monolayer in the 63.5 mm stirred cell. With the PES (polyethylene sulfone) membrane, it was possible to remove the media applying 150 mbar for 20-30 sin the case of 50×106 cells while 30-60 seconds and 200 mbar were necessary to remove the media on 60×106 cells. With the PCTE (polycarbonate track etched) membrane it took 60 seconds at 250 mbar for the lower cell concentration. In the case of 100×106 cells after 2 min at 250 mbar the medium will still present on the filter membrane. To remove this the pressure was raised to 1 bar for 10 seconds and then decreased to normal levels (100 mbar). This was done several times to aid media removal.
Positive pressure was tested with the unmodified filter holder (
With the modified filter holder (
The type of filter used to generate the monolayer was investigated. The filters differed in material, hydrophobicity and pore size. The materials tested included PES and Polycarbonate track etched filters, PCTE, hydrophobic and hydrophilic membrane coating, sizes included 13, 25 mm, 47 mm and 63 mm diameter and pore size ranged from 0.4 μm to 1.2 μm diameter. Also tested were PETE (Polyester), Silver and Gold membranes (See below Table).
The filters were assessed for formation of an even monolayer, efficiency in removal of the culture medium and recovery of the cells from the filter membrane. Dynabeads were used as representative of cells to assess monolayer formation. In addition, expanded T-cells were used to assess monolayer formation, recovery and viability post monolayer formation.
The PES filters were investigated and it was found these filters enabled formation of an even monolayer and efficient removal of the culture medium. However, recovery of cells from the filter membrane was low (50%). The PCTE, track-edge filters, resulted in improved cell recovery (50-90%) from the filter membrane (
Atomization to Enable intracellular Delivery of mRNA to T-Cells
Investigation of the LB-100 spray head demonstrated a target area of 60 mm in diameter. Force analysis of the LB-100 was carried out (
To optimise LB-100 spray delivery, the height of the spray head to the target area was adjusted. Distance in the range of 30 mm to 160 mm from spray head tip to the target area was investigated. The optimal range of distance was found to be within 60 to 100 mm from tip of the spray head to the target area. Uptake increased at the lower distance and decreased as you moved further away.
To optimise LB-100 spray delivery, the air pressure was varied in the range of 1 to 6 bar, with 2.5 to 3.0 bar found to be the optimal range for intracellular delivery. GFP mRNA delivery was reduced at pressures lower than 2.5 bar and cell viability was reduced at pressures higher than 3.0 bar. Increasing the air pressure did increase the effective target area.
To optimise LB-100 spray delivery, the volume delivered was varied in the range of 10 to 300 μl with a volume between 80 to 100 μl found to be optimal for intracellular delivery. 5-10 ml cell suspension of human primary T cells in the range of 0.4-10×106/ml was added to the stirred cell unit (Merck Millipore; PCTE filter, 0.4 μm or 1 μm pore size). Positive pressure in the range of 100-150 mbar was applied for 20-50 s to foi>lr the cell monolayer. The cell monolayer was sprayed with 10-300 μl of delivery solution containing 0.1 μg/μl of GFP mRNA and incubated for 2 min. Stop solution (1 ml) was added and incubated for 30 s following this, culture medium (4 ml) was added to the filter membrane. Cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry between 17-24 hours later.
To increase delivery efficiency, an assessment of the optimal number of hits comparing 1 and 2-hit strategies was performed. Data demonstrated an increase in delivery efficiency when cells received a second hit. 5-10 ml cell suspension of human primary T cells in the range of 0.4-10×106/ml was added to the stirred cell unit (Merck Millipore; PCTE filter, 0.4 μm or 1 μm pore size). Positive pressure in the range of 100-150 mbar was applied for 20-50s to form the cell monolayer. The cell monolayer was sprayed with 80-100 μl of delivery solution containing 0.1 μg/μl of GFP mRNA and incubated for 2 min. Stop solution (1 ml) was added and incubated for 30 s following this, culture medium (4 ml) was added to the filter membrane. For the 2-hit strategy the cells were incubated for 2 hours before the spray process was repeated (as described above). Cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry between 17-24 hours later. The double hit process resulted in increased delivery efficiency (
To increase delivery efficiency, the number of cells seeded on the filter membrane was investigated. Cell density of 13×103 cells/mm2 were seeded in the stirred cell unit (Merck Millipore; PCTE filter, 0.4 μm or 1 μm pore size). Positive pressure in the range of 100-200 mbar was applied for 10-50 s to faun the cell monolayer. The cell monolayer was sprayed with 80-100 μl of delivery solution containing 0.1 μg/μl of GFP mRNA and incubated for 2 min. Stop solution (1 ml) was added and incubated for 30 s, followed by addition of culture medium (4 ml) to the filter membrane. Cells were incubated overnight at 37° C. and 5% CO2 in a humidified incubator and assessed for GFP fluorescence by flow cytometry between 17-24 hours later.
The duration of the spray was investigated. This was achieved by adjusting the opening time of the valves which control the flow of air and payload to the atomiser. Spray duration between 280-700 ms were tested.
In some embodiments, to facilitate and to enhance the exposure of cells to permeabilizing solution a filter membrane can be vibrated before, after, and/or during, delivery of the permeabilizing solution. To assist in the formation of a monolayer of cells on a filter membrane, the membrane can be vibrated before, after, and/or during, formation of the monolayer.
The vibration may be brought about by an eccentric rotating mass (ERM) system or a linear resonant actuator (LRA) system. For example, in a preferred embodiment, 1, 2 or 3 actuators (LRA) corresponding to the X,Y and Z axis can be attached to the membrane or a corresponding membrane holder (e.g., membrane holders 10006, 10106) such that the membrane vibrates when the actuators are activated. An advantage of the LRAs is that each axis of vibration can be driven independently. Accordingly, controllable vibration patterns may be developed on the membrane. Additionally, identification of mechanical resonance points due to physical characteristics of the membrane can improve a degree of control that can be exhibited over the membrane. In some embodiments, a 3 axes accelerometer device can be mechanically coupled to the membrane and/or membrane holder to provide data characterizing motion and/or excursion of the membrane and/or membrane holder. Data from the accelerometer can be used within a feedback control system to control actuation of the LRAs. For example, the accelerometer can be used to monitor vibrations of the membrane and/or membrane holder. In some embodiments, data from the accelerometer can be used as a control feedback signal to adjust vibrations generated by the LRAs. For example, data from the accelerometer can be used to generate an error signal between a desired vibrational pattern and an achieved vibrational pattern. As an example, driving vibrational frequencies can be detennined based on a stiffness of the membrane and/or sizes of cells on the membrane. An example vibrational pattern can brought about with sinusoidal signals at 3000 Hz on the x and y axes and no signal on the z axis. The excursions can be lrnrn peak to peak and the x and y driving waveforms can be coherent with no phase difference between them. Many other patterns are possible including ones that lead to swirling and/or shaking in the x, y, and/or z axes.
The current subject matter can include a non-viral, vector-free method that achieves intracellular delivery through gentle reversible permeabilization. The current subject matter can include 1) a permeabilising solution that contains a low dose of ethanol as the permeabilising agent and 2) a means of applying the delivery solution to the target cells in a dropletised form. The technology provides tight control over the volume, time and pressure at which the penneabilising solution is applied to the cells and this enables high levels of delivery efficiency as well as cell viability to be attained.
The steps of the process can include: a monolayer of target cells is generated; supernatant is removed from the cells; the cargo is mixed with the delivery solution and applied to the cells in a dropletised form and incubated for 2 min; during this period, the ethanol pen-neabilises the cell membrane and the cargo diffuses into the cell; cargo enters directly into the cytoplasm in an endocytosis-independent manner; a ‘stop’ solution is then applied to the cells and incubated for 30 sec—this acts to dilute the pcnneabilising delivery solution and allows the cell membrane to begin to reseal; culture medium is then added to complete the process.
While the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
The patent and scientific literature referred to herein establishes the knowledge that is available to those with skill in the art. All United States patents and published or unpublished United States patent applications cited herein are incorporated by reference. All published foreign patents and patent applications cited herein are hereby incorporated by reference. All other published references, documents, manuscripts and scientific literature cited herein are hereby incorporated by reference.
While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the scope of the invention encompassed by the appended claims.
This application is a continuation of U.S. application Ser. No. 16/471,466 filed on Jun. 19, 2019, which is a national stage application filed under 35 U.S.C. § 371, of International Patent Application No. PCT/IB17/001713, filed Dec. 21, 2017, which claims the benefit of and priority under 35 U.S.C. § 119 to U.S. Provisional Patent Application Number 62/438,298 filed Dec. 22, 2016, U.S. Provisional Patent Application Number 62/528,963 filed Jul. 5, 2017, and U.S. Provisional Patent Application Number 62/536,831 filed Jul. 25, 2017, the entire contents of each of which is hereby expressly incorporated by reference herein.
| Number | Date | Country | |
|---|---|---|---|
| 62536831 | Jul 2017 | US | |
| 62528963 | Jul 2017 | US | |
| 62438298 | Dec 2016 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16471466 | Jun 2019 | US |
| Child | 17337165 | US |
