Introduction

In this project, we intended to establish a synthetic biology-based effective HIV-curing system with less side-effects. The key goal is to integrate CRISPR/Cas system into human blood system to protect CD4+ cells against viral infection. The gRNA is designed to target the relative conserved regions in HIV viral genome and inactivate its biological activity. Since viral vectors seem to be of limited use in gene therapy strategies (e.g., potential pathogenicity), there is in dire need of a simple, efficient system for targeting cell-specific introduction of nucleic acids. By using non-viral DNA delivery system such as A-B-toxin-GAL4 fusion protein, we can deliver plasmids encoding gRNA into the CD4+ cells and readily attack multiple HIV genome sites simultaneously with the most up-to-date knowledge of HIV epidemic.

Background

HIV (Human immunodeficiency virus)

HIV is the trigger of the lethal disease AIDS. It replicates in and kills T cells, weakening human immune system and allows life-threatening opportunistic infection and cancers to thrive. HIV infects vital cells in the human immune system such as helper T cells (especially CD4+ T cells), macrophages, and dendritic cell. As a retrovirus, HIV reverse transcribes its genome and integrated it into the host cell genome after infection. Figure 1 demonstrates the schematic structure of HIV virus (Source: Wikipedia).

Traditional therapies such as chemotherapy and radiotherapy can control the development of the disease but not eradicate the virus. The chronic inflammation and immune dysfunction caused by long-term chemotherapy and radiotherapy may also lead to non-AIDS morbidity and mortality (Kiem, Jerome, Deeks, & McCune, 2012). The process of reverse transcription is extremely error-prone, and the resulting mutations may lead to drug resistance or allow the virus to evade the body's immune system.

CRISPR/Cas system

CRISPR/Cas (Clustered regularly interspaced short palindromic repeats/CRISPR-associated system) is originally a self-protecting mechanism in bacteria against external DNA such as virus genome or plasmids. It uses CAS complex to cut the external viral or plasmid DNA and integrating a short DNA segment into the CRISPR loci in the bacteria genome. This short DNA segment will be transcribed into pre-crRNA and bind to another CAS endonuclease called Cas9 with the help of tracrRNA. The Cas9 endonuclease cuts the external DNA in the existence of not only crRNA but also a special recognizing sequence at the 3’ end of the target DNA called PAM (Protospacer Adjacent Motif). When the same external DNA invades next time, the Cas9-tracrRNA-crRNA complex will recognize and cut it in order to destroy its biological activity. Figure 2 demonstrates the mechanism of Type II CRISPR/Cas system in bacteria (Mali, Esvelt, & Church, 2013). Dr. George Church (Mali, Yang, et al., 2013) and Dr. Feng Zhang (Cong et al., 2013) both have successfully transfected Type II CRISPR-Cas system into human cells, which is the foundation of this project.

PiggyBac (PB) transposon system

PiggyBac (PB) transposon is a mobile genetic element that efficiently transposes between vectors and chromosomes via a "cut and paste" mechanism but leave no “footprint”. PB transposase in this system recognizes the transposon-specific inverted terminal repeat sequence (PB5 & PB3 in Figure 5) located on both end of transposon vector and efficiently moves the contents from the original sites and efficiently integrates them into TTAA chromosomal sites. Figure 3 demonstrates the working mechanism of PB transposon system (Source: Wikipedia; Author: Transposagenbio).

A-B toxin

A-B toxin are two-component exotoxin secreted by a number of pathogenic bacteria. The complexes contain two subunits called A and B. A subunit is the active portion that is poisonous to host cells. B subunit has a translocation domain and cell receptor binding domain, which helps the A subunit going into the cell through endosomes. Figure 4 shows how Anthrax toxin (a kind of A-B toxin) enters into human cells (Source: Wikipedia; Author: Y tambe).

Experiment design

Constructing EGFP-Cas9 expressing cell line

The program aims to endow the human cell the capacity of resisting the infection of HIV by introducing the CRISPR/Cas9 system into the human cell. To test the efficiency of the Cas9 and explore the optimal conditions of the system, we need a reporter to indicate whether the Cas9 functions and the targeted sites are cut off and destructed. So a cell line integrated with EGFP and Cas9 gene is firstly constructed in a similar way. We use PiggyBac transposon to transfect Hela cell line for permanently expressing Cas9 protein. Once the proper gRNA is delivered into these cells, Cas9 binds to the gRNA and start to cut the complementary DNA strand. The vector design is based on Feng Zhang lab’s and Wei Huang lab’s plasmids.

Transfecting the cell line with gRNA-encoding plasmid

Cas9 uses gRNA, a 23nt short RNA fragment which binds to its complementary target and 'guide' Cas9 to cut the target DNA. We first check the efficiency of this system at first. We construct a plasmid based on Zhang Feng Lab’s pX330 plasmid that encodes a chimeric guide RNA scaffold and mCherry reporter gene followed by a NLS (nucleus leading sequence). It also contains 0, 2, 5 or 7 UAS sequences which are necessary for the vehicle’s recognition and binding (See Future applications – A-B toxin based gRNA shuttle for details).

The chimeric guide RNA scaffold is used to insert gRNA. We acquired the gRNA for EGFP from Wei Huang’s lab and put it into our constructed plasmid. Figure 8 shows the design of chimeric guide RNA scaffold (Cong et al., 2013).

In this way, with the ratio of reduced green fluorescence and the quantity of red fluorescence we can roughly obtain the efficiency of the CRISPR-Cas system we created. And finally, we reconstruct the plasmid but this time with the sgRNA targeting HIV and test its efficacy.

Deliver gRNA plasmids by A-B toxin-based shuttle

CRISPR/Cas system needs two essential parts for normal function: Cas9 and gRNA. We’ve seen a paper published in July that We choose a non-viral DNA delivery system which is based on modified A-B toxin. The chimeric fusion protein mainly comprises 3 parts: target cell-specific binding domain, a translocation domain and a nucleic acid binding domain. The target cell-specific binding domain recognizes the EGF (epidermal growth factor) receptors on the cell surface. The translocation domain enhances nucleic acid escape from the cellular vesicle system and thus to augment nucleic acid transfer. The nucleic acid binding domain, which derives from the yeast GAL4 transcription factor, can carry plasmids with UAS (Upstream Activation Sequence) sequences into cells in vivo. Several research groups from Germany to Taiwan (Gaur, Gupta, Goyal, Wels, & Singh, 2002) (Chen et al., 2000) (Fominaya, Uherek, & Wels, 1998) have achieved this goal. We are requesting the plasmid encoding TEG vehicle from a Germany research group. Figure 9 shows the schematic representation of the TEG fusion gene in the E.coli expression plasmid pWF47-TEG; Figure 10 shows the schematic representation of the GD5 fusion gene in the E.coli expression plasmid pSW55-GD5 (Wels, Winfried 63110 Rodgau (DE)).

Plasmid & experiment design

Before using this delivery system, we need to check the delivery efficiency of this protein system at first. So, firstly, we construct a plasmid that carries a sgRNA for EGFP, several UAS sequences which are necessary for the vehicle’s recognition and binding and a mCherry gene sequence followed by a NLS (nucleus leading sequence). Figure 9 demonstrates the plasmid we construct.

The construction is based on the plasmid backbone of Zhang Lab’s pX330. There are two BbsI restriction enzyme sites between U6 strong promoter and U6 terminator in which we can insert sgRNA. Once sgRNA is inserted, the two BbsI sites disappear and the sgRNA can’t be changed anymore. Figure 10 shows how sgRNA replacement is blocked once BbsI sites are used.

CBh is a eukaryotic promoter, followed by mCherry and 3*NLS. NLS makes red fluorescent protein enter into cell nucleus after expression. By means of PCR and molecular cloning, we can change the number of UAS, a sequence of 17bp which is recognized and bound by GAL4 protein. The sgRNA we used in this plasmid is for EGFP, to collaborate with the Cas9 system and EGFP gene that we have integrated into Hela cell line. In this way, we can visualize how many plasmids are transformed into nucleus by detecting the quantity of red-fluorescence-emitting cells. And with the ratio of reduced green fluorescence and the quantity of red fluorescence we can roughly obtain the efficiency of the CRISPR-Cas system we created. And finally, we reconstruct the plasmid but this time with the sgRNA targeting HIV and test its efficacy.

gRNA design and Modeling

Written by Rongpeng Li and Fan Jiang

gRNA design

gRNA is a 23nt short RNA fragment (not include tracrRNA) which binds to its complementary target and 'guide' Cas9 to cut the target DNA. Since we would like to destroy the HIV virus inside human body, a gRNA sequence that matched a part of HIV conserved region best but have few off-target matches in the human genome is desired. However, designing a gRNA for a human-infective virus is difficult due to the very large difference in the genome size. For virus like HIV, it is even more difficult because HIV can mutate in a very high rate. So finding a perfect gRNA is not realistic. However, finding a group of specific quasi-conservative sequences (gRNA) which are able to target one or more species of HIV is possible.

Our search for the sequence roughly followed the process described in George M. Church's paper (Mali, Yang, et al., 2013). We modified it slightly to fit our own purpose. We first used bioinformatics method to find the quasi-conservative regions in the HIV-1 whole genome reference library by NIH. From the candidates, we selected the region around 720bp from beginning of the genome (aligned), in the less-selected region slightly off the LTR.

We then used the online tools of Feng Zhang's Lab at MIT to find our desired gRNA composition. We also did some calculation based on phenomenological energy calculation to estimate the stability and effectiveness of our gRNA sequences (Hsu et al., 2013). The tool shows that almost no off-target binding will occur. BLAST was used to further confirm the results. We also analyzed the structure of the resulted gRNA, which shows an approximate free energy of -1.4kJ (Zuker, 2003).

For detailed information, see our Modeling page.

Modeling

本段需要重写

The last part is a maverick design which models the inter-cell interaction of T cells to simulate the cell swarm behaviors, our ultimate goal is to determine the desired ratio of cured T cell to recover from a HIV virus carrier.

Our last part focuses on the modeling of the cell interaction. We want to extract a mathematical critical ratio of restored T cells if we want a HIV carrier to be cured. We attempt to apply graph theory and Particle Swarm Optimization to tackle this problem.

Future applications

Written by Yicong Tao

Stably transfect hematopoietic stem cells

August PNAS reveals the possibility of gene therapy in retrovirus diseases

Using CRISPR/Cas to stably transfect itself in a safe locus instead of using Piggybac

In vivo verification

The project is intended to treat retrovirus diseases. Let’s take AIDS as an example to see what’s going to happen. First, stably transfect hematopoietic stem cells with the plasmid which encodes Cas9 protein. Second, we use bioinformatics to screen out a 20bp conserved regions in HIV DNA which has no conservation in human genome. Then, constructing a plasmid which encodes the gRNA sequence. When the human body is infected by AIDS, using non-viral DNA transfecting methods (e.g. A-B toxin based shuttle) to deliver the plasmid into human somatic cells (especially CD4+ cells) and the CRISPR/Cas system is activated. The Cas9 protein recognizes viral DNA with the help of gRNA and cut the target sequence, causing double strand break (DSB). The DSB is then repaired by the non-homologous end joining mechanism in the cell but with high error rate, causing frame-shift mutation and gene knockout. The viral protein synthesis is stopped and further infection is impossible, providing potentiation for eradicating AIDS.

References

Chen, T. Y., Hsu, C. T., Chang, K. H., Ting, C. Y., Whang-Peng, J., Hui, C. F., & Hwang, J. (2000). Development of DNA delivery system using Pseudomonas exotoxin A and a DNA binding region of human DNA topoisomerase I. Applied Microbiology and Biotechnology, 53(5), 558-567.

Cong, L., Ran, F. A., Cox, D., Lin, S. L., Barretto, R., Habib, N., . . . Zhang, F. (2013). Multiplex Genome Engineering Using CRISPR/Cas Systems. Science, 339(6121), 819-823. doi: DOI 10.1126/science.1231143

Fominaya, J., Uherek, C., & Wels, W. (1998). A chimeric fusion protein containing transforming growth factor-alpha mediates gene transfer via binding to the EGF receptor. Gene Ther, 5(4), 521-530. doi: 10.1038/sj.gt.3300614

Gaur, R., Gupta, P. K., Goyal, A., Wels, W., & Singh, Y. (2002). Delivery of nucleic acid into mammalian cells by anthrax toxin. Biochemical and Biophysical Research Communications, 297(5), 1121-1127. doi: Pii S0006-291x(02)02299-4 Doi 10.1016/S0006-291x(02)02299-4

Hsu, P. D., Scott, D. A., Weinstein, J. A., Ran, F. A., Konermann, S., Agarwala, V., . . . Zhang, F. (2013). DNA targeting specificity of RNA-guided Cas9 nucleases. Nature Biotechnology, 31(9), 827-+. doi: Doi 10.1038/Nbt.2647

Mali, P., Esvelt, K. M., & Church, G. M. (2013). Cas9 as a versatile tool for engineering biology. Nat Methods, 10(10), 957-963. doi: 10.1038/nmeth.2649

Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., . . . Church, G. M. (2013). RNA-guided human genome engineering via Cas9. Science, 339(6121), 823-826. doi: 10.1126/science.1232033

Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res, 31(13), 3406-3415. doi: Doi 10.1093/Nar/Gkg595