Microfluidic systems and methods for lipoplex-mediated cell transfection

Abstract

Systems and methods for transfection using a microfluidic device are disclosed. Microdroplets encapsulate cells, transfection molecules, and cationic lipid transfection reagent. Droplet chaotic advection in a rendering channel of the system results in a uniform lipid-DNA complex (lipoplex) formation, which can improve gene delivery efficacy. The shear stress exerted on cell membranes during the chaotic mixing increases membrane permeability, which when combined with the co-confinement of cell and lipoplex, improves transfection efficiency of the cell. The systems and methods can be used for a variety of applications such as gene therapy, in vitro fertilization, regenerative medicine, cancer treatment, and vaccines.

Claims

1. A method of transfecting a cell (101), said method comprising: a. providing a microfluidic system (100), said system (100) comprising a microfluidic device (110) comprising: i. a first aqueous phase channel (115a); ii. a second aqueous phase channel (115b); iii. a combining channel (118) having an inlet end and a shearing outlet end, wherein the first aqueous phase channel (115a) and the second aqueous phase channel (115b) are fluidly connected to the inlet end of the combining channel; iv. a continuous phase channel network (116) comprising a first continuous phase channel (117a) and a second continuous phase channel (117b), wherein an outlet end of each continuous phase channel is fluidly connected to the shearing outlet end of the combining channel thus forming a droplet shearing junction (205) having a constricting droplet pinch-off orifice; and v. a rendering channel (120) having an inlet end fluidly connected to the droplet shearing junction (205), wherein at least a section of the rendering channel comprises a winding serpentine channel (125); b. introducing a first aqueous solution and the second aqueous solution into their respective aqueous phase channels (115a, 115b), wherein the first aqueous solution comprises cells (101) and transfection molecules (101), wherein the second aqueous solution comprises transfection reagents (103); c. combining the first and second aqueous solutions at the combining channel (118); d. introducing a continuous phase fluid into the continuous phase channels (117a, 117b); e. combining the continuous phase fluids with the combined aqueous solutions at the droplet shearing junction (205); f. shearing the combined aqueous solutions to form droplets (210) at the constricting droplet pinch-off orifice, wherein at least one cell (101), at least one transfection molecule (102), and at least one transfection reagent (103) are encapsulated in one droplet (210), wherein a flow rate of the combined aqueous solutions and a flow rate of the continuous phase fluids are adjusted such that the droplets (210) are formed in a dripping regime, wherein a ratio of the flow rate of the continuous phase fluids to the flow rate of the combined aqueous solutions is at least 5, wherein a capillary number (Ca) of the dripping regime is Ca>0.1, wherein in the dripping regime, the constricting droplet pinch-off orifice squeezes and exerts shear stress on the at least one cell (101) as it passes through the constricting droplet pinch-off orifice, thereby increasing membrane permeability due to cell deformation; and g. flowing the droplets (210) through the rendering channel (120), wherein flow of the droplets through the winding serpentine channel (125) induces chaotic advection that causes the transfection molecules (102) and transfection reagents (103) to form lipoplexes, and applies shear stress to the cells (101), thereby increasing membrane permeability to allow for transport of the lipoplexes through the cell membrane, thus transfecting the cells (101).

2. The method of claim 1, wherein the shearing outlet end is tapered.

3. The method of claim 1, wherein the first continuous phase channel (117a) and the second continuous phase channel (117b) are disposed on opposite sides of the combining channel (118).

4. The method of claim 1, wherein a section of the first continuous phase channel connected to the shearing outlet end and a section of the second continuous phase channel connected to the shearing outlet end are orthogonal to the combining channel (118).

5. The method of claim 1, wherein the rendering channel (120) is fluidly connected to the outlet ends of the continuous phase channels.

6. The method of claim 1, wherein the inlet end of the rendering channel has an arrowhead shape such that the inlet end tapers at the droplet shearing junction (205), gradually widens, and then narrows as it transitions to a straight portion of the rendering channel.

7. The method of claim 1, wherein the continuous phase fluid comprises an oil.

8. The method of claim 1, wherein the transfection reagents (103) comprise cationic lipids, helper lipids, or a combination thereof.

9. The method of claim 1, wherein the transfection molecules (102) comprise DNA, RNA, protein, a carbohydrate, a small molecule, or a combination thereof.

10. The method of claim 1, wherein the transfection molecules (102) comprise CRISPR-CAS transfection molecules.

11. The method of claim 10, wherein the CRISPR-CAS transfection molecules are DNA vectors encoding single guide RNA (sgRNA), DNA vectors encoding CAS nuclease gene, DNA vectors encoding both sgRNA and CAS nuclease gene, sgRNA or other RNA molecules, CAS nuclease or other protein molecules, sgRNA-CAS complexes, or other DNA or RNA and protein complexes.

12. The method of claim 10, wherein the CRISPR-CAS transfection molecules modify a gene by utilizing a targeting sequence complementary to a target DNA sequence in the gene, wherein when the targeting sequence interacts with the target DNA sequence, a CAS nuclease is guided to the target sequence and cleaves the target DNA at the target sequence to produce double strand breaks, which are then repaired by the cell, thus leading to modification of the gene.

13. The method of claim 12, wherein said modification of the gene is addition, deletion, replacement, or mutation.

14. The method of claim 1, wherein the cells (101) are eukaryotic cells, prokaryotic cells, or a combination thereof.

15. The method of claim 14, wherein the prokaryotic cells are bacterial cells.

16. The method of claim 14, wherein the eukaryotic cells are animal cells, plant cells, algae cells, fungal cells, or a combination thereof.

17. The method of claim 1, wherein the cells (101) are protoplasts, pollen grains, microspores, tetrads, or a combination thereof.

18. The method of claim 1, wherein fluid flow in the device is pressure-driven.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) The features and advantages of the present invention will become apparent from a consideration of the following detailed description presented in connection with the accompanying drawings in which:

(2) FIG. 1A is a schematic view and mechanism of a system of the present invention. Section (A) shows a schematic illustration of the droplet microfluidics-based single-cell lipofection platform. The zoom-in views of the circled regions are shown in the upper right corner: a single-cell is co-encapsulated with plasmid and Lipofectin® is shown in section (B), thereafter negatively-charged plasmid and positively-charged Lipofectin self-assemble into lipoplex during chaotic advection as shown in section (C), which enters the co-encapsulated single cell by endocytosis shown in section (D).

(3) FIG. 1B shows droplet generation and co-encapsulation of single K562 cells with plasmids and Lipofectin in picoliter-droplets. Scale bar: 100 μm.

(4) FIG. 1C shows a bright-field snap-shot of droplets' chaotic advection in the winding channel. The encapsulated single K562 cells are highlighted by red circles. Scale bar: 100 μm.

(5) FIG. 1D shows Fluo-4 emitting strong fluorescence after mixing with Ca.sup.2+. Fluorescence intensity increased and eventually saturated during the droplet chaotic advection in the rapid mixing region.

(6) FIGS. 2A-2E shows mechanisms of improved transfection efficiency via droplet chaotic advection in the winding channel. FIG. 2A shows chaotic mixing of dye and PBS during droplet advection in the winding channel. FIG. 2B shows DLS size measurement of lipoplexes generated by droplet mixing using the present platform as compared to conventional vortexing. FIG. 2C is a fluorescence intensity histogram of 1,000 live single K562 cells analyzed via flow cytometry 48 h after transfection with pcDNA3-EGFP plasmid using droplet microfluidics-prepared and vortexing-prepared lipoplexes. FIG. 2D shows average lipofection efficiencies of K562 cells, as indicated by the percentages of EGFP positive cells, transfected via bulk lipofection protocol using either vortexing-prepared () or droplet microfluidics-prepared () lipoplexes, and via droplet lipofection using either a straight mixing channel () or a winding mixing channel () FIG. 2E is a numerical simulation showing symmetric and steady vortices when droplets move in the straight channel. FIG. 2F is a numerical simulation illustrating asymmetric and constantly-changing vortices during droplet advection in the winding channel. FIG. 2G shows a fluorescence intensity histogram of 1,000 live single K562 cells analyzed via flow cytometry 48 h after transfection with pcDNA3-EGFP plasmid using the present droplet-lipofection platform with a winding channel and a modified platform with an equal-length straight channel. Scale bar: 50 μm.

(7) FIGS. 2H-2I shows cell deformation after experiencing shear stress when squeezing through the droplet generation pinch-off. FIG. 2H shows time-lapse micrographs showing the deformation of a K562 cell when it passed through the pinch-off of the flow-focusing droplet generation orifice. The pictures were taken at a frame rate of 45,000 pictures-per-second. FIG. 2I shows time-lapse images showing the shear stress at the pinch-off during the droplet generation calculated by numerical simulation. Scale bar: 50 μm.

(8) FIG. 3A shows fluorescence intensity of 1,000 live single K562 (left), THP-1 (middle), or Jurkat (right) cells analyzed via flow cytometry 48 h after transfection of pcDNA3-EGFP plasmid via either bulk incubation with vortexing-prepared lipoplex or the present droplet microfluidics-based single-cell lipofection platform.

(9) FIG. 3B displays bright-field (top) and fluorescent (bottom) images of single EGFP-transfected K562 cells at different fluorescence intensity values. The images were taken when individual cells passed through the detector in the ImageStream flow cytometer. Cells in the bulk lipofection group had various fluorescence intensities over a broad range, whereas cells in the droplet lipofection group had much smaller intensity variation. Scale bar: 7 μm.

(10) FIG. 3C shows an average transfection efficiency compared between the present droplet lipofection approach and the conventional bulk lipofection as measured by the percentage of EGFP-positive cells. Three repeat experiments were conducted for each cell line.

(11) FIG. 3D shows cell viability compared between the present droplet lipofection approach and the conventional bulk lipofection as measured by the percentage of propodeum iodide-negative cells. Three repeat experiments were conducted for each cell line.

(12) FIG. 3E displays bright-field and fluorescent images of K562 cells 48 hrs after transfection of pcDNA3-EGFP plasmid via droplet lipofection (left) and bulk lipofection (right). Scale bar: 100 μm.

(13) FIGS. 4A-4D shows targeted knockout of TP53BP1 in K562 cells through the delivery of pLentiCRISPR.v2-sgTP53BP1 plasmid via droplet lipofection. FIG. 4A is a schematic illustration of the targeted gene knockout via the CRISPR/CAS9 mechanism. FIG. 4B is an annotated sequence map of the pLentiCRISPR.v2-sgTP53BP1 plasmid constructed for targeted knockout of the TP53BP1 gene in K562 cells. FIG. 4C shows an sgRNA sequence (SEQ ID NO: 1) and PAM sequence (SEQ ID NO: 2) targeting the 2nd exon of the TP53BP1 gene. FIG. 4D shows representative RT-qPCR amplification curves of every 1,000 K562 cells after the TP53BP1 knockout by either droplet lipofection or bulk lipofection. The Ct value of the bulk-lipofection group was very close to that of the non-transfected group, whereas the Ct value of the droplet-lipofection group was significantly higher, indicating a higher efficiency of gene knockout.

(14) FIGS. 5A-5D show fluorescence intensity histograms from flow cytometry of K562 (FIG. 5A), THP-1 (FIG. 5B), Jurkat (FIG. 5C), and HeLa (FIG. 5D) cells in the negative control group.

(15) FIGS. 5E-5F show a non-limiting embodiment of the droplet-lipofection platform with a straight mixing channel (FIG. 5E) and droplets encapsulating single K562 cells and lipoplexes running through this straight channel (FIG. 5F). Scale bar: 100 μm.

(16) FIGS. 6A-6B show fluorescence intensity v.s. normalized cell-count frequency histograms (FIG. 6A) and the average EFGP transfection efficiencies (FIG. 6B) of HeLa cells transfected via droplet lipofection and conventional bulk lipofection.

(17) FIGS. 7A-7D show RT-qPCR results for analyzing the knockout efficiency of TP53BP1 in K562 cells via the CRISPR/CAS9 mechanism. In FIGS. 7A-7C, the RT-qPCR amplification curves of every 1,000 K562 cells after the TP53BP1 knockout by either droplet lipofection or bulk lipofection in three repeating experiments. The Ct value of the bulk-lipofection group was very close to that of the non-transfected group, whereas the Ct value of the droplet-lipofection group was significantly higher, indicating a higher efficiency of gene-knockout. FIG. 7D shows a standard curve for calibrating the absolute number of TP53BP1 mRNA molecules.

DETAILED DESCRIPTION OF THE INVENTION

(18) Following is a list of elements corresponding to a particular element referred to herein: 100 microfluidic system 101 cells 102 transfection molecules 103 transfection reagents 110 microfluidic chip/device 115a first aqueous phase channel 115b second aqueous phase channel 116 continuous phase channel network 117a first continuous phase channel 117b second continuous phase channel 118 combining channel 120 rendering channel 125 serpentine/winding channel portion 205 droplet shearing junction 210 droplets

(19) According to some embodiments, the present invention features methods and systems for efficient and consistent transfection through co-encapsulation of single cells, transfection molecules such as plasmids and DNA-targeting RNA and Cas9 complexes, and transfection reagents such as cationic lipids and cationic polymers, into monodispersed microdroplets and rapid mixing by chaotic advection.

(20) Transfection Reagents

(21) The methods and systems of the present invention feature the use of transfection reagents, which are co-encapsulated with cells and transfection molecules (e.g., plasmids, DNA-targeting RNA and Cas9 complexes or encoding vectors etc.) in microdroplets. In some embodiments, the transfection reagents comprise cationic lipids. Cationic lipids or other appropriate lipid aggregates can function to facilitate introduction of macromolecules, such as DNA, RNA, and proteins, into living cells. Since the membranes of most cells have a net negative charge, cells do not readily take up anionic molecules, particularly those of high molecular weight. Cationic lipids aggregate to and bind polyanions, such as nucleic acids, tending to neutralize the negative charge. The effectiveness of cationic lipids in transfection of nucleic acids into cells is thought to result from an enhanced affinity of cationic lipid-nucleic acid aggregates for cells, as well as the function of the lipophilic components in membrane fusion.

(22) Cationic lipids, which are amphiphilic molecules with cationic groups in the head group, are well known to one of ordinary skill in the art. One well-known example is Lipofectamine®. Other examples include poly-1-lysine (PLL) and polyethyleneimine (PEI). The present invention is not limited to the aforementioned cationic lipids or other commercially available cationic lipids (e.g., Lipojet™, LipoD293™, etc.), as any appropriate cationic lipid may be considered, e.g., glycerol derived lipids, cholesterol derived lipids, pyridine derived lipids, malonic acid derived lipids, etc. In some embodiments, the transfection molecule comprises cationic lipids and one or more helper molecules (e.g., helper lipids).

(23) Transfection Molecules

(24) Nucleic acid, e.g., DNA or RNA, is the most commonly transfected molecule. However, the present invention is not limited to transfection of DNA or RNA. In some embodiments, the molecule that is transfected is DNA, RNA, a protein, a carbohydrate, a small molecule (e.g., a drug), the like, or a combination thereof. In some other embodiments, the transfection molecule may be a targeting complex comprising a DNA-targeting RNA bound to Cas9 polypeptide, also referred to as a Cas9 nuclease, which forms a DNA-targeting RNA and Cas9 complex. The Cas9 may be naturally-occurring, a derivative, or modified Cas9. In other embodiments, the transfection molecule may be a targeting complex comprising a DNA-targeting RNA bound to a site-active polypeptide other than Cas9. In other embodiments, the transfection molecule may be a targeting complex that can be used in CRISPR-Cas gene editing. For example, the transfection molecule is the DNA-targeting RNA and Cas9 complex for CRISPR-Cas9. In some other embodiments, the transfection molecule for CRISPR-CAS9 may be a DNA vector encoding sgRNA, a DNA vector encoding CAS9 nuclease gene, DNA vector encoding both sgRNA and CAS9 nuclease gene, an sgRNA or other RNA molecules, a CAS9 nuclease or other protein molecules, an sgRNA-CAS9 complexes, or other DNA or RNA and protein complex.

(25) Transfected Cells

(26) Any particular cell type from any organism may be used in the methods and systems of the present invention, namely any cell suitable for transfection. In some embodiments, the cells may be wild type cells or genetically modified cells. In other embodiments, the cells may be cells harboring one or more mutations, healthy cells, diseased cells or unhealthy cells, etc. For example, in some embodiments, the cells may be prokaryotic cells (e.g., bacteria, archaebacteria, etc.). In other embodiments, the cells may be eukaryotic cells such as single-celled eukaryotes, fungal cells (e.g. yeast, mold, etc.), animal cells, mammalian cells (e.g. cells from a human, non-human primate, rodent, rabbit, sheep, dog, cat, etc), and non-mammalian cells (e.g. cells from insects, reptiles, amphibians, birds, etc.).

(27) In some embodiments, the cells used in the present invention may be other eukaryotic cells such as plant cells or algal cells. Non-limiting and non-exhaustive examples of plant cells include cells from corn, soybean, wheat, cotton, grass, flowering plants, fruit-bearing plants, trees, tuberous plants, potatoes, root plants, carrots, peanut, nuts, beans, legumes, and squashes. It is to be understood that the term “plant cell” encompasses all types and stages of plant cells and is not limited to the aforementioned examples. Non-limiting and non-exhaustive examples of algal cells include cells from Chlorella sp., Nannochloropsis sp, and Botryococcus sp. It is to be understood that the term “algal cell” encompasses all types of algal cells and is not limited to the aforementioned examples. One of the distinguishing characteristics that plant and algal cells have over animal cells is a cell wall that surrounds a cell membrane to provide rigidity, strength, and structure to the cell. The cell wall may be comprised of polysaccharides including cellulose, hemicellulose, and pectin. Similar to plant and algal cells, the fungal cells also have a cell wall, which may be comprised of polysaccharides including glucans, mannans, and chitin. In some embodiments, the microfluidic systems and methods described herein may allow for transfection through the cell wall as well as the cell membrane.

(28) In other embodiments, the cells used in the present invention may be protoplasts, which are intact plant, bacterial or fungal cells that had its cell wall completely or partially removed using either mechanical or enzymatic means.

(29) In yet other embodiments, the cells used in the present invention may be a tetrad. The term “tetrad” is used to herein to refer to a single structure comprised of four individual physically attached components. A “microspore” is an individual haploid structure produced from diploid sporogenous cells (e.g., microsporoyte, pollen mother cell, or meiocyte) following meiosis. A microspore tetrad refers to four individual physically attached microspores. A “pollen grain” is a mature gametophyte containing vegetative (non-reproductive) cells and a generative (reproductive) cell. A pollen tetrad refers to four individual physically attached pollen grains.

(30) Methods and Systems for Transfection

(31) Referring to FIG. 1A, the present invention features a microfluidic system (100) for cell transfection. According to some embodiment, the system (100) may comprise a microfluidic chip (110) with a first aqueous inlet channel (115a) and a second aqueous inlet channel (115b). The first aqueous inlet channel (115a) and second aqueous inlet channel (115b) fluidly connect into a central combining channel (118). Cells (101) and plasmids (102) are suspended in a buffer (e.g., Opti-MEM reduced serum buffer) and are introduced into the microfluidic chip (110) via the first aqueous inlet channel (115a). Cationic lipids (103) (e.g., Lipofectamine®, Lipojet™, LipoD293™, etc.) are introduced to the microfluidic chip (110) via the second aqueous inlet channel (115b). The chip (110) further comprises at least one continuous phase inlet channel (116) that fluidly connects to a terminal end of the central combining channel (118), thus forming a droplet shearing junction (205). In some embodiments, the continuous phase may comprise oil, such as mineral oil or alternative to mineral oil. At the shearing junction (205), the continuous phase shears the two co-flowing aqueous phases (the cells (101)/plasmids (102) and the cationic lipids (103)), generating single-cell encapsulating droplets (210).

(32) In some embodiments, the encapsulating droplets (210) subsequently enter into a rendering channel (120). In one embodiment, as shown in FIG. 1B, an inlet end of the rendering channel has an arrowhead-shape such that the inlet end tapers at the droplet shearing junction, gradually widens, and then abruptly narrows to a width of a straight portion of the rendering channel. The width of the straight portion is sufficient to allow for the droplets to enter the straight portion. The rendering channel further comprises a serpentine channel portion (125), in which chaotic advection induces rapid mixing and shear, resulting in lipoplex formation and transfection of the cell. In some embodiments, the system can be implemented in gene therapy, RNA sequencing, development of regenerative medicine, cancer treatments, or vaccines, in vitro fertilization, or an in vitro assay.

(33) In some embodiments, the system (100) of the present invention may be constructed from a variety of materials. For example, in some embodiments, the system (100) is constructed from a material comprising a polymer, a plastic, glass, the like, or a combination thereof. As a non-limiting example, in some embodiments, the system (100) comprises a polydimethylsiloxane (PDMS) based microfluidic chip fabricated using standard soft-lithography methods with an SU8 master mold on a silicon substrate generated by photolithography. The system (100), e.g., the microfluidic chip (110), may be constructed with any appropriate material.

(34) The present invention is not limited to a single unit (e.g., microfluidic chip). In some embodiments, the system may comprise a plurality of microfluidic chips, referred to as a microfluidic array. For instance, multiple experiments may be performed in parallel using the microfluidic array.

(35) As used herein, the microfluidic devices employ fluid volumes on the scale of microliters (10.sup.−6) to picoliters (10.sup.−12) that are contained within sub-millimeter scale channels. The structural or functional features may be dimensioned on the order of mm-scale or less. For example, a diameter of a channel or dimension of a chamber may range from <0.1 μm to greater than 1000 μm. Alternatively or in addition, a length of a channel may range from 0.1 μm to greater than cm-scale. Alternatively or in addition, the serpentine channel section may comprise two or more winding turns. For example, the serpentine channel section may comprise 2 to 20 winding turns.

(36) As previously discussed, the methods and systems of the present invention provide a more uniform formation of lipoplex using chaotic mixing inside mono-dispersed micro-droplets compared to lipoplex formation using vortexing or hand-shaking. Without wishing to limit the present invention to any theory or mechanism, it is believed that the uniform formation of lipoplex reduces the transfection variation between cells and improves the overall intracellular delivery efficiency. Further, the co-confinement of a single cell and the lipoplex in microdroplets helps to breaks the diffusion limitation in bulk transfection so that the cell and lipoplex are in closer contact. Further still, the shear stress exerted on the cell membrane during the chaotic advection helps improve the membrane permeability. The entire process is cell-friendly; neither genomic disruption nor viability damage is applied to cells.

Experimental Example

(37) The following is a non-limiting example of the present invention, in particular, to a microfluidic system and use thereof. The example is for illustrative purposes only and not intended to limit the invention in any way. Equivalents or substitutes are within the scope of the invention.

(38) Chip Fabrication and Experimental Setup

(39) The presented microfluidic device was fabricated via soft lithography. A 30-μm high SU-8 master mold was patterned on a silicon wafer using standard photolithography, whereafter liquid polydimethylsiloxane (PDMS) mixture comprising a base and curing agent at a 10:1 ratio was cast on the mold and cured for 3 h in a convection oven at 65° C. for complete cross-linking. The PDMS microchannel was then peeled off from the mold and irreversibly bonded to a clean glass slide after oxygen plasma treatment for 60 s. The sealed chip was baked at 120° C. overnight to secure the channel hydrophobicity. All the reagents were driven into the microfluidic chip through polymer tubing and syringe pumps.

(40) Plasmid Preparation

(41) A pcDNA3-EGFP vector (Addgene plasmid #13031) encoding enhanced green fluorescence protein (EGFP) was propagated in Escherichia coli (E. coli), extracted, and purified using the QIAprep Spin Miniprep Kit. The plasmid was dissolved in EB buffer and stored at −20° C. until use. For targeted gene knockout, a 20-bp sgRNA sequence targeting the 2nd exon of TP53BP1 is CAGAATCATCCT-CTAGAACC (SEQ ID NO: 1). This sgTP53BP1 sequence was cloned into a pLentiCRISPR v2 vector encoding the S. pyogenes Cas9 protein, and the re-constructed plasmid was purchased from GenScript. Every time before the transfection experiment, the plasmid concentration was measured by the absorbance at 260 nm using a NanoDrop Spectrophotometer.

(42) Cell Culture and Lipofection

(43) K562 (human chronic myelogenous leukemia cell line), THP-1 (human acute monocytic leukemia cell line), and Jurkat (human acute T cell leukemia cell line) cells were purchased from American Type Culture Collection (ATCC), and cultured in RPM11640 medium supplemented with 10% fetal bovine serum (FBS). 0.05 mM of 2-mercaptoethanol was added as a metabolic supplement for THP-1 cell culture. HeLa cells were purchased from ATCC and cultured in DMEM medium supplemented with 10% FBS. Cells were cultured in a humidified incubator at 37° C. with 5% CO.sub.2, and passaged every 2-3 days following standard protocols. A day before transfection, cells were re-suspended in 10 mL fresh media at 5×10.sup.5 viable cells/mL in a T-75 flask, to maintain the cells in the logarithmic (Log) growth phase.

(44) Before transfection, cells were washed once with Opti-MEM reduced serum medium and re-suspended in Opti-MEM at 10.sup.7 cells/mL. For lipofection via droplet microfluidics, the cell suspension was added with 2 μg per 100 μL of pcDNA3-EGFP plasmid and introduced into the microfluidic chip via one inlet; cationic lipid Lipofectin® was diluted in Opti-MEM at a concentration of 4 μL per 100 μL and introduced through the other inlet. The two co-flowing aqueous phases were sheared by FC-40 (Fluorinert™) with 5% 1H, 1H, 2H, 2H-perfluoro-1-octanol into single-cell encapsulating droplets and experienced chaotic mixing in the winding channel. The emulsion was collected and centrifuged at 500 rpm for 30 s to separate the aqueous phase containing cells and lipoplexes from the oil phase. For lipofection via the conventional bulk method, DNA suspension (2 μg DNA per 100 μL Opti-MEM) was added to the Lipofectin® suspension (4 μL Lipofectin® per 100 μL Opti-MEM), gently vortexed and added to the cell suspension. For both of the lipofection methods, the cells and lipoplexes were incubated at 37° C., 5% CO.sub.2 for 24 h, and thereafter, the cells were re-suspended in complete growth media for another 24 h before transgene expressing investigation.

(45) Flow Cytometry

(46) For quantitative analysis of the transfection efficiency and the cell viability, cells were washed and re-suspended in PBS supplemented with 2% FBS at a concentration of 2×10.sup.7 cells/mL 48 h after initial experiment. 1 μg/mL propidium iodide was added for dead cell staining. The cell suspension was analyzed using the ImageStream Mark II Imaging Flow Cytometer at 60× magnification under the laser excitation of 488 nm, 150 mW. The data containing the single-cell bright-field and fluorescent images of each individual cell were analyzed using the IDEAS® software package.

(47) Setup of the Reverse Transcription-Quantitative Real-Time PCR (RT-qPCR)

(48) The S. pyogenes Cas9 enzyme generates double-strand breaks at the single guide RNA (sgRNA) targeted locus, which can lead to gene knockout so that the mRNA at this locus will not be transcribed. Here, the TB53BP1 knockout efficiency was analyzed by RT-qPCR using the Cells-to-CT™ 1-Step Power SYBR® Green Kit following the manufacturers protocol. Firstly, 1,000 transfected K562 cells were lysed in the lysing buffer. Thereafter, for a reaction volume of 20 μL, 2 μL cell lysate, 10 μL qRT-PCR Mix, 0.16 μL RT Mix, 200 nM forward primer, and 200 nM reverse primer were added. A Chromo4 qPCR instrument was used with the following thermal cycling setup: 48° C. for 30 min (reverse transcription), 95° C. for 10 min (polymerase activation), 45 cycles of 94° C. for 15 s and 60° C. for 1 min (amplification). Melting curves were generated by increasing the temperature from 60° C. to 95° C. and holding for 10 s after each 0.5° C. temperature increment. The forward primer sequence was 5′-GGTTCTAGAGGATGATTCTG-3′ (SEQ ID NO: 3), and the reverse primer sequence was 5′-TTCAGG-ATTGGACACAAC-3′ (SEQ ID NO: 4).

(49) Numerical Simulation

(50) Numerical modeling was adopted to analyze the chaotic mixing of droplets passing through the straight/winding channel, and the shear stress at the flow focusing droplet generation junction. 2D transient modeling of fluid flows for both analyses was performed using COMSOL Multiphysics. Specifically, the level-set multiphase model was employed to accurately track the interface between the aqueous and the oil phases. The density and viscosity of the oil phase were set as 1.855 g/mL and 3.40 mPa.Math.s according to the propriety of FC-40; while the values of 1.007 g/mL and 0.74 mPa.Math.s were chosen for the aqueous phase according to the property of Opti-MEM. The surface tension between the two phases and the contact angle were set at 0.01 N/m and 180°, respectively. Triangular mesh elements were mainly used for meshing the geometries. For analyzing the chaotic advection in the winding channel, a total of 100,000 triangular elements were used, whereas a total of 20,000 mesh elements were utilized to analyze the shear stress at the flow focusing droplet generation junction. For both analyses, the mesh was refined near the walls of the microchannel for better accuracy.

(51) Platform Design

(52) An embodiment of the droplet microfluidics-based single-cell lipofection platform of the present invention is illustrated in FIG. 1A, section (A). Two co-flowing aqueous phases, one for cell and plasmid suspension and the other for cationic lipid solution, are pinched off at a flow-focusing geometry. As shown in section (B), at this junction, single cells are co-encapsulated with cationic lipids and plasmids in monodisperse microdroplets and experience chaotic mixing in the winding channel. While undergoing chaotic mixing, plasmid and cationic lipid self-assemble into lipoplexes, as shown in section (C), which enter the co-encapsulated single cell through endocytosis, as shown in section (D). The concentrations of the suspension cells (10.sup.7 cells/mL), plasmids (2 μg per 100 μL), and cationic lipids (4 μg per 100 μL) were set based on the manufacturer's protocol. A 1% (v/v) Pluronic F-68 was added to the cell suspension to avoid cell aggregation. The composition of the oil phase, FC-40 with 5% 1H, 1H, 2H, 2H-perfluoro-1-octanol (v/v), was optimized so that the droplets were able to stay apart during the chaotic advection, but were easy (500 rpm, 30 s) to fuse together and separate into two phases for cell and lipoplex collection. In some embodiments, fluorocarbon oil (i.e., FC-40) may be used as the encapsulation phase instead of hydrocarbon oil (e.g., mineral oil). Fluorocarbon oil has higher gas permeability and much lower solubility of organic molecules, which can permit high cell viability and minimal loss of the transfection reagents into the oil phase. At a flow rate of 1.2 μL/min for each of the two aqueous phases, and 6.0 μL/min for the oil phase, the resulting single cell-lipoplex co-encapsulating droplets had a diameter of 52 μm (FIG. 1B, 1C).

(53) Droplet production was in the dripping regime with a production rate of 0.85 kHz, where droplet breakup was shear-dominated and the fluid interface was detached from the channel surface. Due to the limitation imposed by Poisson statistics for random cell loading, the single-cell encapsulation efficiency of the platform was about 18%. In alternative embodiments, a higher single-cell loading efficiency may be achieved if the platform is coupled with inertial cell ordering in a curved channel, or inertial cell focusing in a long, high-aspect-ratio microchannel, or one-cell-to-one-droplet releasing by the hydrodynamic micro-vortices at the droplet pinch-off interface.

(54) The cationic lipid used herein is Lipofectin®, a non-viral vector for cell transfection, which comprises a mixture of positively charged lipid N-(1-(2,3-dioleyloxy)propyl)-n,n,n-trimethylammonium chloride (DOTMA), and helper lipid dioleoyl-phophotidylethanolamine (DOPE) at a 1:1 (w/w) ratio. Cationic lipids form lipoplexes spontaneously with polyanionic nucleic acids upon electrostatic interaction, and the resulting complexes interact with the cell membrane and are internalized through endocytosis. Upon endosomal maturation, a fraction of DNA escapes and enters the nucleus to elicit gene expression. Alternatively, DNA is degraded within the lysosome. The fusogenic behavior of DOTMA results in functional intracellular delivery of polynucleotide in a manner that bypasses degradative enzymes present in the lysosomal compartment. While DOPE facilitates the intracellular release of DNA, its amine group interacts with DNA phosphate groups, making the lipoplex more susceptible to disassembly; besides which, it rapidly fuses with the endosomal lipid bilayer, promoting DNA endosomal escape.

(55) Chaotic Mixing in Microdroplets

(56) Chaotic advection is induced in the unsteady, time-dependent flows inside the droplets moving through a winding microchannel of a rendering region, which results in rapid mixing on a millisecond timescale. As demonstrated in FIG. 1D, Fluo-4 and Ca.sup.2+ were encapsulated and mixed by chaotic advection, emitting strong green fluorescence as the droplet moved along the rendering channel.

(57) Due to the chaotic mixing inside micro-droplets, the lipoplexes generated from the platform were monodisperse with a mean diameter of 277 nm, which was in the proper size range for internalization by endocytosis. The avoidance of the non-uniformity of lipoplexes prepared via bulk preparing processes (e.g., hand shaking or vortexing) was confirmed by dynamic light scattering (DLS, FIG. 2B). As a result, the proportion of lipoplexes that were too large or too small for intracellular delivery was minimized. K562 cells were transfected with pcDNA3-EGFP plasmid using both droplet microfluidics-prepared lipoplexes and vortexing-prepared lipoplexes following the standard lipofection protocol, and analyzed by flow cytometry 48 h after transfection. As shown in the fluorescence intensity (x-axis) versus cell count (y-axis) histogram of every 1,000 live transfected K562 cells (FIG. 2C), cells transfected with droplet microfluidics-prepared lipoplexes demonstrated a clear shift towards a higher fluorescence intensity indicating a higher EGFP transfection efficiency, compared to cells transfected with vortexing-prepared lipoplexes. To compensate for auto-fluorescence, surface binding and endocytosis, the EGFP transfection threshold, i.e., the vertical line in the histogram, was defined such that less than 1% of cells in the negative control group (cells transfected with pcDNA3.1 plasmid, a vector without any fluorescence protein-encoding sequences, following the standard lipofection protocol) fell into the effective EGFP transfection region in the histogram (FIGS. 5A-5D). Based on three repeating experiments transfecting K562 cells following the standard lipofection protocol, the transfection efficiency was 9.0±1.2% when using droplet microfluidics-prepared lipoplexes, which was significantly higher than using vortexing-prepared lipoplexes (4.8±0.9%, FIG. 2D), verifying the importance of the lipoplex monodispersity on transfection efficiency.

(58) To compensate for auto-fluorescence, surface binding, and endocytosis, K562, THP-1, Jurkat, and HeLa cells were transfected with pcDNA3.1 plasmid, a vector without any fluorescence protein-encoding sequences, following the standard lipofection protocol as the negative control, and analyzed via flow cytometry 48 h after transfection. The sample fluorescence intensity v.s. normalized cell-count frequency histograms of the 4 types of cells in the negative control group were shown in FIGS. 5A-5D. The EGFP transfection threshold (vertical line in the histogram) was defined such that less than 1% of cells in the negative control fell into the effective EGFP transfection region (unshaded region) in the histogram. The EGFP transfection efficiency of a sample thus corresponded to the percentage of live cells that were in the effective transfection region.

(59) When a droplet is moving in a straight channel, due to the equal shearing interaction between the flow and the side walls, two steady and symmetrical vortices are induced within the left and the right (along the flow direction) halves of the droplet (FIG. 2E). This results in poor mixing since the streamlines from each half do not cross each other. However, when a droplet is moving in a winding channel, because of the asymmetric shear experienced by the droplet at each turning portion, two asymmetric vortices fold and stretch the fluid inside the droplet, as illustrated by numerical simulation (FIG. 2F). Thus, chaotic advection and rapid mixing occur inside droplets because crossing of the streamlines becomes possible at each turn. The effectiveness of chaotic advection can be quantified by striation thickness (s.sub.t), the distance over which mixing has to occur by diffusion. For a droplet passing through a winding channel, the striation thickness decreases exponentially according to s.sub.t(n)=s.sub.t(0)×2.sup.−n, as explained in the Baker's Transformation, where n is the number of stretching, folding and reorienting cycles, s.sub.t(0) is the initial striation thickness, and s.sub.t(n) is the striation thickness after n cycles. The chance of cell-lipoplex collision was significantly increased due to the confinement of a single cell with lipoplexes inside picoliter-volume micro-droplets and the intensive chaotic mixing, which overcame the diffusion limitations in the bulk volume. To compare the lipofection efficiency via droplet chaotic mixing in a winding channel versus droplet mixing in a straight channel, K562 cells were transfected with pcDNA3-EGFP plasmid using both the droplet-lipofection platform and a modified platform with the winding channel replaced by an equal-length straight channel (FIGS. 5E-5F). As shown in the flow cytometry histogram (FIG. 2G), the EGFP positive cells transfected via the platform with a straight mixing channel had a broader fluorescence intensity distribution, which was suggested to be caused by the insufficient droplet mixing. As shown in FIG. 2D, the transfection efficiency using the straight channel droplet-lipofection platform was 10.3±1.6%, which was higher than bulk lipofection (4.8±0.9%) but much lower than cells transfected through the present platform with a winding channel (51.8±3.3%). The results indicate that chaotic mixing in the winding channel is necessary for achieving the optimum transfection efficiency and consistency.

(60) Cell Deformation at the Droplet Pinch-Off

(61) As is shown in FIG. 2H, an originally round and spherical suspension cell was deformed and stretched after passing through the droplet generation pinch-off orifice in the platform, since it was exposed to rapid constriction and shear. The shear stress at the droplet pinch-off was as high as 514 dyne/cm.sup.2 as calculated by numerical simulation (FIG. 2I). Transient membrane disruptions or holes may be caused by the rapid mechanical deformation of a cell, as it passes through a constriction smaller than the cell diameter or is subjected to high shear stresses. The degree of disruption and the size and frequency of the holes are determined by the imposed shear and compressive forces. In the present platform, apart from deforming cells at the droplet pinch-off, cationic lipids were incorporated as the non-viral vector to facilitate the delivery of large protein-encoding plasmids with big backbones by lipoplex endocytosis. Among the three barriers of lipoplex-mediated gene delivery, i.e., the cell, endosomal and nucleus membranes, the present platform was capable of overcoming the cell membrane barrier by increasing membrane permeability through cell deformation at the droplet pinch-off.

(62) Increased Transfection Efficiency and Consistency for Suspension Cells

(63) To compare the transfection efficiency between droplet microfluidics-based single-cell lipofection and conventional bulk lipofection, three types of suspension cells, i.e., K562, THP-1, and Jurkat, were transfected via both approaches and analyzed by flow cytometry 48 h after transfection with the pcDNA3-EGFP plasmid. As shown in the fluorescence intensity (x-axis) versus cell count (y-axis) plots of every 1,000 live transfected single cells for each cell lines (FIG. 3A), the droplet-lipofection histogram was significantly shifted towards a higher fluorescence intensity compared to the bulk-lipofection histogram, which demonstrated an overall higher EGFP expression level, and therefore a higher transfection efficiency for the droplet-lipofection group. The exact transfection efficiencies were calculated and compared in FIG. 3C. Using the platform, the transfection efficiency increased from 2.3±0.4% to 52.5±5.7% for Jurkat cells, from 3.8±0.5% to 46.3±5.4% for THP-1 cells, and from 4.8±0.9% to 51.8±3.3% for K562 cells. Referring to FIG. 3D, with respect to cell viability, the present platform realized a 10-fold increase in lipofection efficiency for hard-to-transfect suspension cells with a competitive cell viability as compared to the standard bulk approach. It has also demonstrated a better performance as compared to other non-viral methods that reported at most 32% transfection efficiency. As an examination of the platform's performance on adherent cells, which are easier to transfect compared to suspension cells, HeLa cells were also ran through the present droplet-lipofection device to transfect them with the same pcDNA3-EGFP plasmid, (FIG. 6A-6B). There was a clear increase in transfection efficiency when using droplet lipofection (75.5±4.6%) compared to using the conventional bulk lipofection protocol (35.1±3.6%), which supports that rapid cell-squeezing through droplet pinch-off together with chaotic mixing in the confined micro-droplet improved transfection efficiency.

(64) Another significant result was that the histograms of the bulk transfected cells (FIG. 3A) had a broad distribution ranging from a very low fluorescence intensity to an extremely high intensity, which was also verified by the single-cell bright-field and fluorescent images taken when they passed through the flow cytometer (FIG. 3B). In contrast, cells transfected via droplet lipofection had a narrower fluorescence intensity distribution (FIG. 3A), and there were no super bright cells compared to the bulk method (FIG. 3E). Therefore, the present platform provided a much lower cell-to-cell transfection variability and a higher transfection consistency, which are important performance metrics in gene therapy. This transfection consistency was realized via droplet microfluidics and not in the bulk process, as the cell-encapsulating microdroplets generated on chip were monodisperse with a size deviation less than 2%, enabling quantitative and precise control of the reagents and manipulation applied to each individual cell. Benefiting from the chaotic advection and cell-squeezing through the droplet pinch-off, the present platform enabled ˜10 times higher transfection efficiency than bulk and demonstrated a better performance as compared with other reported non-viral methods for suspension cell transfection.

(65) CRISPR-Cas9 Gene Editing

(66) The platform of the present invention was implemented in CRISPR-CAS9-mediated targeted gene editing. The CRISPR-Cas9 system has been broadly used in biomedical research and clinical applications because of its high-efficiency and high-specificity in targeting the locus of interest. A 20-bp single-guide RNA (sgRNA) directs the Cas9 nuclease to introduce double-strand breaks at the sequence-specific genome locus, whereafter non-homologous end joining DNA-repairing mechanism is triggered, which generates gene mutation at the targeted locus (FIG. 4A). The mutation will often block the normal gene expression and results in gene knockout. As shown in FIG. 4C, a sgRNA sequence (SEQ ID NO: 1) targeting the 2nd exon of the TP53BP1 (tumor suppressor p53 binding protein 1) gene was designed and cloned in between a U6 promoter sequence and gRNA scaffold of the pLentiCRISPR v2 vector, which also carried the sequence of S. pyogenes CAS9 nuclease (FIG. 4B). The constructed plasmids were delivered into K562 cells via both droplet lipofection and the bulk method, and RT-qPCR of the targeted locus was performed for every 1,000 single cells 48 h after the initial delivery. As plotted in the representative RT-qPCR amplification curves (FIG. 4D) of three repeating experiments (FIGS. 7A-7C), the amplification curve of the bulk-lipofection group was very close to that of the non-transfected group, whereas the amplification curve of the droplet-lipofection group shifted towards a higher cycle-threshold (Ct) value, indicating a higher efficiency of gene knockout. The Ct value was 31.3±0.2 for the non-transfected group, 31.8±0.3 for the bulk-lipofection group, and 33.9±0.6 for the droplet-lipofection group.

(67) Upon calibration using the established standard curve (FIG. 7D), wherein the correlation between the absolute number of TP53BP1 mRNA molecules (n) and the Ct value was: Log.sub.10.sup.n=(41.35−Ct)/3.59, the corresponding copy number of the target mRNA molecules was 630±61 for the non-transfected group, 457±83 for the bulk-lipofection group, and 119±51 for the droplet-lipofection group. Therefore, the estimated TP53BP1 knockout efficiency through the delivery of pLentiCRISPR.v2-sgTP53BP1 plasmid was 27±13% when using bulk lipofection, and 81±8% when using droplet lipofection. However, as the Cells-to-CT™ 1-Step Power SYBR Green Kit was used for this experiment, in which cell lysing, mRNA extraction and RT-qPCR were all integrated into one assay, there was an unavoidable loss of mRNA molecules during cell lysing and mRNA extraction, which caused an over-estimation of the gene knockout efficiency. Overall, the estimated knockout efficiency by droplet lipofection was satisfactory for this difficult-to-transfect lymphoma cell line that could not be achieved by current bulk lipofection methods.

(68) Thus, based on the examples and results described herein, the present invention provides a droplet microfluidics-based single-cell transfection platform for lipoplex-mediated efficient and consistent plasmid delivery for hard-to-transfect suspension cells. In this platform, single cells were co-encapsulated with cationic lipids and plasmids in monodisperse micro-droplets, and chaotic mixing resulted in monodisperse lipoplexes for consistent and efficient transfection. Using the platform, the pcDNA3-EGFP plasmid delivery efficiency improved from ˜5% to ˜50% for all of the three tested suspension cell lines, i.e., K562, THP-1, Jurkat, with significantly reduced cell-to-cell variation, compared to the bulk method. The platform was also utilized in CRISPR/CAS9-mediated gene editing and demonstrated efficient targeted knockout of TP53BP1 gene in K562 cells. Without wishing to limit the present invention to a particular theory or mechanism, the platform had an order of magnitude higher transfection efficiency and much lower transfection variability (higher consistency) These features may be attributed to: 1) the chaotic mixing generating monodisperse lipoplexes in the proper size range for endocytosis, 2) confining a single-cell with lipoplexes in a picoliter-droplet plus chaotic advection to overcome the diffusion limitations in the bulk reaction volume while generating intensive lipoplex-cell collision, and 3) the membrane permeability increasing due to cell deformation resulting from the exerted shear stress as it passed through the droplet pinch-off orifice. Lipoplex-mediated single-cell transfection via droplet microfluidics can have broad applications in gene therapy and regenerative medicine by providing higher transfection efficiency and lower cell-to-cell variation for hard-to-transfect cells, such as lymphoma and hematopoietic cells.

(69) As used herein, the term “about” refers to plus or minus 10% of the referenced number.

(70) Various modifications of the invention, in addition to those described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. Each reference cited in the present application is incorporated herein by reference in its entirety.

(71) Although there has been shown and described the preferred embodiment of the present invention, it will be readily apparent to those skilled in the art that modifications may be made thereto which do not exceed the scope of the appended claims. Reference numbers recited in the claims below are exemplary and solely for ease of review and examination of this patent application by the patent office only, and are not limiting in any way. The reference numbers are not intended in any way to limit the scope of the claims to the particular features having the corresponding reference numbers in the drawings. Therefore, the scope of the invention is only to be limited by the following claims. In some embodiments, the figures presented in this patent application are drawn to scale, including the angles, ratios of dimensions, etc. In some embodiments, the figures are representative only and the claims are not limited by the dimensions of the figures. In some embodiments, descriptions of the inventions described herein using the phrase “comprising” includes embodiments that could be described as “consisting of”, and as such the written description requirement for claiming one or more embodiments of the present invention using the phrase “consisting of” is met.