Junghae Suh

Efficient active transport of gene nanocarriers to the cell nucleus

The intracellular transport of therapeutic gene carriers is poorly understood, limiting the rational design of efficient new vectors. We used live-cell real-time multiple particle tracking to quantify the intracellular transport of hundreds of individual nonviral DNA nanocarriers with 5-nm and 33-ms resolution. Unexpected parallels between several of natures most efficient DNA viruses and nonviral polyethylenimine/DNA nanocomplexes were revealed to include motor protein-driven transport through the cytoplasm toward the nucleus on microtubules. Active gene carrier transport led to efficient perinuclear accumulation within minutes. The results provide direct evidence to dispute the common belief that the efficiency of nonviral gene carriers is dramatically reduced because of the need for their relatively slow random diffusion through the cell cytoplasm to the nucleus and, instead, focuses the attention of rational carrier design on overcoming barriers downstream of perinuclear accumulation.

Real‐Time Intracellular Transport of Gene Nanocarriers Studied by Multiple Particle Tracking

We used real‐time multiple particle tracking to quantitatively characterize the type and rates of transport of gene nanocarriers within live cells. The heterogeneous cytoplasmic transport of polyethylenimine (PEI)/DNA gene carriers was quantified by tracking their mean‐square displacements over time and classified into active and nonactive transport populations on the basis of their effective diffusivities versus time. Nonactive gene carriers frequently displayed hop‐diffusion trajectories, suggesting a porous cytoplasmic network of flexible biopolymers or sequential attachment and detachment events. Microtubule‐dependent active transport of gene carriers resulted in an effective diffusivity 30‐fold greater than that of nonactive carriers (at a time scale of 3 s). Compared to nonactive carriers in control cells with intact microtubules, microtubule depolymerization enhanced short‐range motion of gene carriers but resulted in similar long‐range transport. Multiple particle tracking characterizes gene carrier transport in complex biological environments and, therefore, may be a useful tool in quantifying rate‐limiting steps in gene delivery within cells and other biological media.

Quantifying the intracellular transport of viral and nonviral gene vectors in primary neurons.

Real-time confocal particle tracking (CPT) was used to compare the transport and trafficking of polyethylenimine (PEI)/DNA nanocomplexes to that of efficient adenoviruses in live primary neurons. Surprisingly, the quantitative intracellular transport properties of PEI/DNA nonviral gene vectors are similar to that of adenoviral vectors. For example, the values of individual particle/virus transport rates and the distributions of particle/virus transport modes (i.e., the percentage undergoing active, diffusive, or subdiffusive transport) largely overlapped. In addition, both PEI/DNA vectors and adenoviruses rapidly accumulated near the cell nucleus in primary neurons despite our finding that PEI/DNA move slower in neurites than in the cell body, whereas adenoviruses move with equal rates in either location. The intracellular trafficking pathways of PEI/DNA and adenoviruses, however, were substantially different. The majority of PEI/DNA trafficked through the endolysosomal pathway so as to end up in late endosomes/lysosomes (LE/Lys), whereas adenoviruses efficiently escaped endosomes. This result suggests that the sequestration of nonviral gene vectors within acidic vesicles may be a critical barrier to gene delivery to primary neurons in the central nervous system (CNS).

Light-Activated Nuclear Translocation of Adeno-Associated Virus Nanoparticles Using Phytochrome B for Enhanced, Tunable, and Spatially Programmable Gene Delivery

Gene delivery vectors that are activated by external stimuli may allow improved control over the location and the degree of gene expression in target populations of cells. Light is an attractive stimulus because it does not cross-react with cellular signaling networks, has negligible toxicity, is noninvasive, and can be applied in space and time with unparalleled precision. We used the previously engineered red (R)/far-red (FR) light-switchable protein phytochrome B (PhyB) and its R light dependent interaction partner phytochrome interacting factor 6 (PIF6) from Arabidopsis thaliana to engineer an adeno-associated virus (AAV) platform whose gene delivery efficiency is controlled by light. Upon exposure to R light, AAV engineered to display PIF6 motifs on the capsid bind to PhyB tagged with a nuclear localization sequence (NLS), resulting in significantly increased translocation of viruses into the host cell nucleus and overall gene delivery efficiency. By modulating the ratio of R to FR light, the gene delivery efficiency can be tuned to as little as 35% or over 600% of the unengineered AAV. We also demonstrate spatial control of gene delivery using projected patterns of codelivered R and FR light. Overall, our successful use of light-switchable proteins in virus capsid engineering extends these important optogenetic tools into the adjacent realm of nucleic acid delivery and enables enhanced, tunable, and spatially controllable regulation of viral gene delivery. Our current light-triggered viral gene delivery prototype may be broadly useful for genetic manipulation of cells ex vivo or in vivo in transgenic model organisms, with the ultimate prospect of achieving dose- and site-specific gene expression profiles for either therapeutic (e.g., regenerative medicine) or fundamental discovery research efforts.

Quantitative nanoparticle tracking: applications to nanomedicine

Particle tracking is an invaluable technique to extract quantitative and qualitative information regarding the transport of nanomaterials through complex biological environments. This technique can be used to probe the dynamic behavior of nanoparticles as they interact with and navigate through intra- and extra-cellular barriers. In this article, we focus on the recent developments in the application of particle-tracking technology to nanomedicine, including the study of synthetic and virus-based materials designed for gene and drug delivery. Specifically, we cover research where mean square displacements of nanomaterial transport were explicitly determined in order to quantitatively assess the transport of nanoparticles through biological environments. Particle-tracking experiments can provide important insights that may help guide the design of more intelligent and effective diagnostic and therapeutic nanoparticles.

An open-hardware platform for optogenetics and photobiology.

In optogenetics, researchers use light and genetically encoded photoreceptors to control biological processes with unmatched precision. However, outside of neuroscience, the impact of optogenetics has been limited by a lack of user-friendly, flexible, accessible hardware. Here, we engineer the Light Plate Apparatus (LPA), a device that can deliver two independent 310 to 1550 nm light signals to each well of a 24-well plate with intensity control over three orders of magnitude and millisecond resolution. Signals are programmed using an intuitive web tool named Iris. All components can be purchased for under

Tunable protease-activatable virus nanonodes.

400 and the device can be assembled and calibrated by a non-expert in one day. We use the LPA to precisely control gene expression from blue, green, and red light responsive optogenetic tools in bacteria, yeast, and mammalian cells and simplify the entrainment of cyanobacterial circadian rhythm. The LPA dramatically reduces the entry barrier to optogenetics and photobiology experiments.

Real-time gene delivery vector tracking in the endo-lysosomal pathway of live cells

We explored the unique signal integration properties of the self-assembling 60-mer protein capsid of adeno-associated virus (AAV), a clinically proven human gene therapy vector, by engineering proteolytic regulation of virus–receptor interactions such that processing of the capsid by proteases is required for infection. We find the transfer function of our engineered protease-activatable viruses (PAVs), relating the degree of proteolysis (input) to PAV activity (output), is highly nonlinear, likely due to increased polyvalency. By exploiting this dynamic polyvalency, in combination with the self-assembly properties of the virus capsid, we show that mosaic PAVs can be constructed that operate under a digital AND gate regime, where two different protease inputs are required for virus activation. These results show viruses can be engineered as signal-integrating nanoscale nodes whose functional properties are regulated by multiple proteolytic signals with easily tunable and predictable response surfaces, a promising development toward advanced control of gene delivery.

Mesophilic and Hyperthermophilic Adenylate Kinases Differ in Their Tolerance to Random Fragmentation

Using live‐cell confocal microscopy and particle tracking technology, the simultaneous transport of intracellular vesicles of the endo‐lysosomal pathway and nonviral polyethylenimine (PEI)/DNA nanocomplexes was investigated. Due to potential problems associated with the use of acid‐sensitive probes in combination with a gene vector that is hypothesized to buffer the pH of intracellular vesicles, the biological location of PEI/DNA gene vectors was revealed by probing their trafficking in cells expressing fluorescent versions of either early endosome antigen 1, a protein that localizes to early endosomes, or Niemann Pick C1, a protein that localizes to late endosomes and lysosomes. Studies directly show that PEI/DNA nanoparticles are actively transported within both early and late endosomes, and display similar overall transport rates in each. Additionally, gene vector transfer between endosomes is observed. Over time post‐transfection, gene vectors accumulate in late endosomes/lysosomes; however, real‐time escape of vectors from membrane‐bound vesicles is not observed. Microsc. Res. Tech., 2012.

Coating barium titanate nanoparticles with polyethylenimine improves cellular uptake and allows for coupled imaging and gene delivery

The extent to which thermostability influences the location of protein fragmentation sites that allow retention of function is not known. To evaluate this, we used a novel transposase-based approach to create libraries of vectors that express structurally-related fragments of Bacillus subtilis adenylate kinase (BsAK) and Thermotoga neapolitana adenylate kinase (TnAK) with identical modifications at their termini, and we selected for variants in each library that complement the growth of Escherichia coli with a temperature-sensitive adenylate kinase (AK). Mutants created using the hyperthermophilic TnAK were found to support growth with a higher frequency (44%) than those generated from the mesophilic BsAK (6%), and selected TnAK mutants complemented E. coli growth more strongly than homologous BsAK variants. Sequencing of functional clones from each library also identified a greater dispersion of fragmentation sites within TnAK. Nondisruptive fission sites were observed within the AMP binding and core domains of both AK homologs. However, only TnAK contained sites within the lid domain, which undergoes dynamic fluctuations that are critical for catalysis. These findings implicate the flexible lid domain as having an increased sensitivity to fission events at physiological temperatures. In addition, they provide evidence that comparisons of nondisruptive fission sites in homologous proteins could be useful for finding dynamic regions whose conformational fluctuations are important for function, and they show that the discovery of protein fragments that cooperatively function in mesophiles can be aided by the use of thermophilic enzymes as starting points for protein design.