1. Introduction
Since Friedmann and Roblin firstly proposed the concept of gene therapy in 1972, it became a promising therapeutic option with a great potential to treat many genetic and acquired diseases [
1,
2,
3]. The primal principle of gene therapy is to introduce foreign genetic material into host cells via suitable vectors, in order to promote the expression of therapeutic proteins or to silence the relevant genes. Several strategies have already been tested in clinical trials, and the used nucleic acids include DNA, message RNA (mRNA), micro RNA (miRNA), short interfering RNA (siRNA), short hairpin RNA (shRNA), small activating RNA (saRNA) and antisense oligonucleotides (ASO), and even patient-derived cellular gene therapy [
4,
5,
6,
7,
8,
9,
10,
11].
As for a delivery platform, viral and non-viral gene delivery systems have been developed and studied through the past several decades, and the utility of these two systems has been greatly investigated. Non-viral gene delivery systems, e.g., liposomes, cationic polymers, and cell-penetrating peptides (CPPs), are considered with properties of lower immunogenic response, safety, higher gene capacity, more stability and more flexibility of chemical design than viral systems [
12]. CPPs typically have 5–30 amino acids and possess the ability to cross the cell membrane. Since Frankel and Pabo discovered the first CPP, trans-activator of transcription (TAT) peptide in 1988, which was originally encoded by human immunodeficiency virus type 1 (HIV-1), there are already more than 1700 CPPs that have been discovered or made nowadays [
13,
14]. CPPs have a variety of applications, such as acting as vectors for nucleic acid condensation, incorporation of functional motif [
15,
16,
17], or even for anti-microbial application [
18,
19].
The RALA peptide (N-WEARLARALARALARHLARALARALRACEA-C) was originated from fusogenic peptides GALA (glutamic acid rich) and KALA (lysine rich), and first reported by McCarthy et al. in 2014 [
20]. It was artificially designed from the KALA peptide by replacing all the lysine residues in KALA by arginine residues, presenting infinite possibilities for nucleic acid therapeutics [
20]. It has been used in dissolving microneedles for DNA vaccination [
21], or condensation of DNA into nanoparticles to be encapsulated within polylactic acid–polyethylene glycol copolymers [
22]. Our team recently collaborated with McCarthy et al. and developed collagen/glycosaminoglycan (GAG) scaffolds activated by RALA complexed matrix metalloproteinase-9 siRNA (siRNA-MMP-9) for improving diabetic foot ulcer healing by reducing the MMP-9 expression from fibroblast [
23].
Histidine is an amino acid that has an imidazole group on the side chain with the pKa value of 6.0, which is lower than that of lysine (pKa 10.53) or arginine (pKa 12.48). Histidine-rich peptides are usually considered as being endosomolytic in nature, as it can accelerate the endosomal escaping process through the proton sponge phenomenon or “flip-flop” effects [
24,
25]. One example of histidine application in CPP was the modification of wild-type S4(13)-PV by adding a five-histidine tail to its N-terminus, resulting in the significantly improved efficacy of peptide-mediated gene silencing in human fibrosarcoma HT1080 cells [
26]. The high transfection efficacy of RALA was mainly due to the arginine in its backbone. Considering RALA has only one histidine in its backbone, in order to unlock the transfection potential of RALA, we aim to develop more advanced CPPs by modulation the histidine and arginine ratio in RALA. Inspired by the evolution history of GALA, KALA and RALA peptides, we designed a series of peptides named HALA (
Table 1). Dependent on the numbers and positions of histidine replacements on the sequence of RALA peptide, we named them HALA1 to HALA4 respectively. HALA1 and HALA2 replace two arginine by histidine on the N-terminal and C-terminal of the sequence respectively, while HALA3 and HALA4 have three replacements on the N-terminal and C-terminal respectively. In this study, we designed HALA1, HALA2, HALA3, and HALA4 for comprehensive in vitro gene transfection study, due to their representativeness of replacing the arginine number (two and three arginine were replaced) and positions of replaced arginine on the peptide sequence (N-terminal and C-terminal).
3. Discussion
Development of high efficacy and safe CPPs are critical for gene therapy [
16,
27,
28]. Arginine is important for cellular internalization and histidine is helpful for endosomal escaping during gene delivery [
29,
30]. With this in mind, in this study, we have successfully developed a series of robust CPPs called HALA, by modulation of the histidine and arginine ratio in a model peptide RALA. Among which, HALA1 and HALA2 demonstrated efficient endosomal capacity, and HALA2 further demonstrated superior cell transfection ability compared to the model peptide. These novel peptides possess high potential in gene therapy application and our design strategy opens a new avenue for improving the transfection efficacy of current designed peptides.
Considering the basic features of CPPs, one should be able to firstly condense the nucleic acid cargo and preserve its completeness while forming nanoparticles. However, the histidine replacements of arginine presented on HALA series peptides in this study reduce the number of positive amino acids, and the arginine might lead to the condensed ability reduction due to its electrostatic interaction. Therefore, we employed a gel retardation assay to analyze the basic factor of CPP on RALA and part of the HALA series peptides. According to the result, we found that with two or three arginine replacements, the condensation ability for the gene cargo of HALA peptides showed little change. All the peptides presented with great condensation ability both in pDNA with 5010 bp and siRNA with only 24 bp, indicated that the HALA peptides are able to condense the gene cargo regardless of the length of it, representing that the HALA series peptides have the potential for becoming a gene delivery platform for multiple kinds of genes.
Particle size and charge of nanoparticles were known to be a critical factors for cellular uptake, and efficient cellular uptake would only occur with submicron positively charged particles and suitable size [
31]. Here in, we employed Dynamic Light Scattering (DLS) and laser Doppler velocimetry to measure the mean hydrodynamic particle size and zeta potential of the nanoparticles by pDNA complexed with RALA and HALA series peptides. The results indicated an appropriate size and charge of nanoparticles, which were in the suitable range.
An efficient functioning platform for gene delivery requires to be non- or low-cytotoxic. Therefore, we employed the Cell Counting Kit-8 (CCK-8) to evaluate the cell viability after regular transfection process. The results indicated that HALA peptides are cytotoxic free at N:P ratios 1 to 12, indicating basically no impact to host cells. This result is similar to other CPPs, therefore again proving that CPPs possess the potential of clinic application owing to their safety and efficiency.
Next, three cell lines were employed to be the transfection target cells for investigating the transfection ability of various peptides. RALA presented great efficacy as predicted in both HeLa and HEK-293T, although A549 was presented as a lesser one. As for the novel HALA series peptides designed by us, the outcomes were various in different specific peptides. HALA2, which got two arginine replaced by histidine on the C-terminal, presented a particularly great transfected efficacy. On HeLa and HEK-293T cells, transfection efficacies of HALA2 were similar to the RALA peptide. Yet, performing on A549, the percentage of EGFP positive cells in HALA2 group was almost two times compared with RALA. This result indicated to us that HALA2 could be considered as a promising gene vehicle for gene delivery. Yet, we also observed the less transfection results from HALA3 and HALA4 groups, which we believed was owing to the extra histidine replacement in the sequence, leading the condensation ability to be reduced while not presenting on the previous gel retardation assay. More cell lines, including normal and tumoral of various origin, should be tested in further experiments for more accuracy outcomes.
When we collected all the data of thev transfection of pDNA in vitro mentioned above, we found an interesting trend demonstrated in all cell lines. HALA2 always presented a higher transfection efficacy compared with HALA1. Similar results were also detected on the peptides of HALA4 and HALA3. Considering the difference of these various peptides, the results indicated that the position of the replaced histidine on the peptide sequence is also a critical factor for developing a novel cell penetrating peptide, N-terminal replacement compared to C-terminal replacement on the peptide sequence will cause a larger impact on the transfection ability, reducing the efficacy of transfection, comparing to the original peptide. Collectively, we could draw the conclusion that the number of histidine replacements and the positions on the peptide sequence are two main factors contributing to the function of CPPs.
Next, we used siRNA-GAPDH as a siRNA cargo to investigate the gene silencing ability of the HALA series peptides and RALA peptide. From the qRT-PCR results we discover that HALA2 is indeed an efficient gene delivery platform for both pDNA and siRNA, which presented the highest gene silencing rate compared to other peptides. As shown from the Western blotting results, even when comparing two commercially available transfection reagents, Lipofectamine® 2000 and Lipofectamine® 3000, HALA2 presented a similar silencing level to Lipofectamine® 3000, which confirms again that HALA2 could be a safe and efficient vector for further application. Yet, more cell lines should be tested by the siRNA-HALA series peptide complex for more comprehensive data. This job is under consideration in our future work plan.
Considering the function of histidine that we applied in this study on the sequence of CPPs, we assumed that the HALA series peptides are all able to acquire an enhanced endosomal escaping capability. Therefore, we employed a known endosomal disruptor chloroquine, which is capable of damaging the formation process of endosome by inhibiting its acidification. As the results showed, HALA1 and HALA2 presented the less relative increase transfection level compared to RALA, yet the HALA3 and HALA4 interestingly presented an increase. A possible reason of this result could be explained by the poor transfection efficacy performed by HALA3 and HALA4 originally on the A549 cell line. While comparing HALA2 and HALA1, HALA2 presented a lesser increase in the result, which indicated to us again that the replaced histidine on the C-terminal of the RALA sequence is the best match with our assumption. Therefore, we believed that the C-terminal replacement of histidine could maximumly enhance the endosomal escaping ability.
Many works have been done by previous researchers for investigating the mechanism of the nanoparticles, consisted by CPPs and gene cargo, crossing the cell membrane. Most studies believed the process is mostly by endocytosis, which requires energy [
32]. Therefore, we created a 4 °C incubational environment for cells which were about to be transfected, trying to inhibit the cell metabolism to cut down the supplement of energy by interfering with the functional temperature. The results unsurprisingly provided the significant evidences to us which indicated that the crossing membrane process indeed requires energy supplement.
Next, we employed several inhibitors related to various endocytosis pathways for a preliminary study of the crossing membrane mechanism of HALA peptides. MβCD was the first inhibitor to be investigated with the transfection process. The results presented that all peptide transection efficacies were decreased. Further experiments incubated with chlorpromazine also presented a result of decrease, but not as much as MβCD. In the group incubated with genistein, the cells presented a similar trend to MβCD. By the results, we can infer that the main endocytosis mechanism of the nanoparticles mentioned in this study is caveolae mediated endocytosis, and it can be inhibited by both MβCD and genistein. Yet there were also other endocytosis pathways that existed, as it was not fully suppressed by these two inhibitors. Further experiments of endocytosis inhibitors on other cell lines are also required for a more precise outcome.
Another interesting outcome drawn by the previous mentioned data is that we realized that the HALA2 peptide presented the least influence caused by any of the inhibitors. A possible explanation for this outcome might be due to the efficient endosome escaping ability of HALA2. With the help of histidine, nanoparticles contain certain numbers of pDNA which reach a certain threshold and are capable of escaping from the endosome efficiently and release pDNA for the upcoming EGFP expression. However, the HALA3 and HALA4, which had three arginine replaced by histidine, presented significant influence by all the inhibitors. These outcomes could be explained by the low transfected rate in the A549 cell line. We would like to put this part into our further research plan.
Other effective CPPs would be employed to study further, for providing evidence that histidine replacements on CPPs is a universal method for enhancing the endosome escaping ability on existing peptides.
Our data demonstrates the impact of histidine replacements on CPPs, pointed out two main factors: that the number of histidine replacements and positions on the peptide sequence (N-terminal or C-terminal) contribute to the final outcomes. The results indicated the merits of HALA series peptides in comparison with the original peptide RALA, through enhancement of CPPs endosome escaping ability. Furthermore, we discovered a novel CPP, HALA2, as indeed a highly effective gene delivery platform for both DNA and RNA in vitro, demonstrating a better efficacy on the HEK-293T and A549 cell lines compared with RALA and Lipofectamine® 3000, indicating a potential translation to clinical application.
5. Materials and Methods
5.1. Preparation of Peptides-Nucleic Acid Nanocomplexes
The RALA peptide and HALA series peptides were produced by Jiangsu Ji Tai peptide Industry Science and Technology Co, Ltd. (Yancheng, China), supplied as a desalted lyophilized powder. Then sterilized ddH2O (Milli-Q, Merck KGaA, Darmstadt, Germany) were used to dissolve the powder and stored in small aliquots at −20 °C. The pCMV-EGFP plasmid contained the Enhanced Green Fluorescent Protein (EGFP) gene under the control of the cytomegalovirus promoter, was purchased from Beyotime (Shanghai, China #D2626). The Human siRNA-GAPDH was purchased from GenePharma (Suzhou, China #A08008), 5′Cy3 modified non-target siRNA and regular non-target siRNA was purchased from Ribobio (Guangzhou, China). The sequence of siRNA-GAPDH is 5′-UGACCUCAACUACAUGGUUTT-3′.
The pCMV-EGFP plasmid was firstly transferred into Trans1-T1 Phage Resistant Chemically Competent Cell from Transgen (Beijing, China #CD501-02), then amplified from overnight bacterial cultures in Lysogeny Broth and obtained by alkaline lysis and purified using a plasmid Maga kit under endotoxin-free conditions (Magen, Guangzhou, China, #P1114-2). The purified plasmid was diluted in TE buffer pH 8.0 to 1mg/mL and quantified by ultraviolet (UV) ray absorption at 260 nm by using NanoDrop (Thermo Fisher Scientific, Waltham, MA, USA) to 1mg/mL and stored in small aliquots at−20 °C.
Peptides-nucleic acid nanoparticles were prepared at various N:P ratios, the molar ratio of positively charged nitrogen atoms in the peptide to negatively charged phosphate in the nucleic acid backbone, in the range of 1 to 12. All aminos with positive charge from various peptides were taken into account for the N:P ratio. The required amount of nucleic acid-peptide complexes was prepared in ddH2O (Milli-Q, Merck KGaA, Darmstadt, Germany) with the order of plasmid or siRNA solution firstly added in ddH2O, then transported with the right amount of peptide solution in it. The final volume was adjusted to 50 μL. The complexes were mixed immediately by using a pipet, and were allowed to stay at room temperature for 30 min for incubation. All nanocomplexes were used immediately after their preparation.
5.2. Cell Culture
The HeLa cell line, A549 cell line, and HEK-293T cell line were kindly provided by Stem Cell Bank, Chinese Academy of Sciences (Shanghai, China). Routine tests confirmed these cells were Mycoplasma-free. They were used as model cells for siRNA and pDNA transfection in this study. All cell lines were maintained as monolayers in high glucose Dulbecco’s Modified Eagle’s Media (DMEM) (Gibco, Waltham, MA, USA) supplemented with 1% fetal bovine serum (FBS) (Gibco, Waltham, MA, USA) and 1% penicillin–streptomycin solution (Invitrogen, Waltham, MA, USA). When the cells reached 80% confluency approximately, they were passaged. All cell lines were cultured under the standard cell culture conditions with the atmosphere of 5% CO2 and 90% humidity at 37 °C.
5.3. Cell Transfection
For pDNA transfection, cells were seeded in 24-well plates at a density of 5 × 104 cells per well and waited for adhesive overnight at 37 °C with 5% CO2. Before the transfection, the original culture media were replaced by 300 μL Opti-MEMTM Reduced Serum Medium (Gibco, Waltham, MA, USA) for 1 h. For pDNA transfection, 50 μL of nanoparticles solution containing 500 ng pDNA was added to the wells and gently mixed with the Opti-MEM. As for siRNA-GAPDH transfection, 50 μL of nanocomplex solution was prepared by calculation of the concentration of siRNA in final culture media to be 40 nM. Cells were then incubated with the nanocomplex for 6h under the condition of 37 °C with 5% CO2, before being replaced with the fresh original complete media.
Cell transfection was repeated with changing the culture environment in 4 °C, or with the addition of either 100 μg/mL chloroquine (Aladdin, Shanghai, China), 5 mg/mL Methyl-β-cyclodextrin (MβCD) (Aladdin, Shanghai, China), 10 mg/mL Chlorpromazine (Aladdin, Shanghai, China) or 10 mg/mL Genistein (Aladdin, Shanghai, China) to investigate the mechanism of endocytosis and endosomal escape of the nanoparticles. Cells transfected with the addiction of various inhibitors or incubated under 4 °C were analyzed by flow cytometer.
5.4. Size and Zeta Potential Analysis of Nanocomplexes
Nanocomplexes were prepared as previous described in various N:P ratio at a range of 1 to 12. The nanoparticles solution was diluted 20 times to 1 mL by ddH2O for further measurement. A Malvern Zetasizer ZS 3000 (Malvern Instruments, Worcestershire, UK) were used to measure the mean hydrodynamic particle size of nanoparticles dispersed in ddH2O by Dynamic Light Scattering (DLS) at 25 °C and zeta potential were using Laser Doppler Velocimetry.
5.5. Gel Electrophoresis of Peptides-Nucleic Acid Nanocomplexes
Nanocomplexes were prepared as previous described at a range of N:P ratios, the molar ratio of positively charged nitrogen atoms in the peptide to negatively charged phosphate in the nucleic acid backbone, from 0 to 12. After mixed with 2 μL loading dye (Thermo Fisher Scientific, Waltham, MA, USA), samples of all groups were electrophoresed through a 1% agarose gel containing GelRed Nucleic acid gel stain (Accurate Biology, Changsha, China #11918) within Tris-acetate (TAE) running buffer at 100 V for 60 min. The siRNA samples were mixed with 2 μL loading dye (Thermo Fisher Scientific, Waltham, MA, USA) before electrophoresed through a 20% polyacrylamide Gel (Thermo Fisher Scientific, Waltham, MA, USA) within Tris-borate-EDTA (TBE) buffer at 120 V for 30 min. Mobility of nucleic acid was visualized using a ChemiDoc Touch (Bio-Rad, Hercules, CA, USA).
5.6. Fluorescence Microscopy
In order to facilitate qualitative analysis of pCMV-EGFP expression which correlated to transfection efficiency, cells after transfection were imaged 24 h following transfection under fluorescein light, using a Leica DMI8 (Leica, Wetzlar, Germany) to visualize.
5.7. Quantification of Peptide Uptake Efficiency by Flow Cytometric Analysis
The amount of uptake efficiency of peptide was quantified by a flow cytometric analysis performed by CytoFLEX (Beckman Coulter, Brea, CA, USA). After transfection processes as described previously, cells were allowed to culture for another 2 days. PBS was used to washed gently twice and the cells were digested with Trypsin (Gibco) for 3 min before collected in 1.5 mL microcentrifuge tubes. Cells were collected by centrifuging under the condition of 3500 rpm/min, and washed with PBS one time before resuspended with FACS buffer. Data were analyzed by using the FlowJo V10 software (BD Life Sciences–FlowJo, Ashland, OR, USA).
5.8. CCK-8 Assays
Cytotoxicity was estimated using a Cell Counting Kit-8 (CCK-8) (Beyotime, #C0037). Cells were seeded in 96-well plates with a density of 5 × 103 cells per well and kept in an incubator overnight for adhesive. A total of 60 μL Opti-MEMTM with nanoparticles, prepared as previous described in various N:P ratios, was added in for 6 h transfection, before replacing the media with fresh one. Cells were allowed to culture for 24 or 48 h in the incubator. Then, PBS was used to wash the well twice before adding the CCK-8 working solution with 90% fresh media and 10% CCK-8 stock solution. Plates were placed in the incubator for 2 h before measuring the absorbance of each well at 450 nm by using a Synergy H1 Hybird Reader (BioTek Instruments, Winooski, VT, USA).
5.9. qRT-PCR
A549 cells were seeded in a 6-well plate with a density of 2 × 105 cells per well, and allowed for culturing overnight for adhesion before transfection. The transfection processes was as previous described. GAPDH gene expression in A549 cell line was evaluated 72 h after transfection by firstly extracted the total RNA by using TRIzol reagents (Invitrogen, USA), then the reverse transcription of first-stand cDNA was using a PrimeScript RT reagent kit (Takara, Kusatsu, Shiga, Japan) following protocols recommended by the manufacturer. Real-time quantitative polymerase chain reaction analyses for mRNA of GAPDH and actin were performed by using Hieff UNICON Universal Blue qPCR SYBR Green Master Mix (YEASEN, Shanghai, China). The sequences of oligonucleotides used are as follows:
Human GAPDH-F: 5′-aggtcggagtcaacggatttg-3′
Human GAPDH-R: 5′-gtgatggcatggactgtggt-3′
Human Actin-F: 5′-ctccatcctggcctcgctgt-3′
Human Actin-R: 5′-gctgtcaccttcaccgttcc-3′
5.10. Western Blot
A549 cells were firstly seeded in a 6-well plate with a density of 2 × 105 cells per well, and allowed for culturing overnight for adhesion before transfection. Total protein in A549 cell line was evaluated 96 h post-transfection as previous described by using lysis buffer. Cell lysis solution were centrifuged at 12,000× g at 4 °C for 15 min. A bicinchoninic acid protein assay kit (Thermo Fisher Scientific) was used to analyze the protein concentrations. The equal amounts of 20 μg of the protein were separated by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis gel and transferred to a nitrocellulose membrane. The membranes were then blocked with 5% nonfat dry milk in Tris-buffered saline and incubated with the following primary antibodies overnight at 4 °C, Anti-β-Actin Mouse Mab (1C7) (Abcam, Waltham, MA, USA) and Anti-GAPDH Mouse Mab (2B5) (Abcam, Waltham, MA, USA) with the concentrations recommended by the manufacturer. After being washed with Tris-buffered saline with 0.1% Tween-20 detergent (TBST) buffer, the membranes were incubated with Rabbit anti-Mouse IgG (H + L) Cross-Adsorbed secondary antibody, the Alexa Fluor 488 (Invitrogen, Waltham, MA, USA), with the concentrations recommended by the manufacturer for 2 h at room temperature. Images of the membranes were visualized and captured using a ChemiDoc Touch (Bio-Rad, Hercules, CA, USA).