Optimization of feline immunodeficiency virus vectors for RNA interference

Concise review on optimized methods in production and transduction of lentiviral vectors in order to facilitate immunotherapy and gene therapy

Lentiviral vectors (LVs) have provided an efficient way to integrate our gene of interest into eukaryote cells. Human immunodeficiency virus (HIV)-derived LVs have been vastly studied to become an invaluable asset in gene delivery. This abled LVs to be used in both research laboratories and gene therapy. Pseudotyping HIV-1 based LVs, abled it to transduce different types of cells, especially hematopoietic stem cells. A wide range of tropism, plus to the ability to integrate genes into target cells, made LVs an armamentarium in gene therapy. The third and fourth generations of self-inactivating LVs are being used to achieve safe gene therapy. Not only advanced methods enabled the clinical-grade LV production on a large scale, but also considerably heightened transduction efficiency. One of which is microfluidic systems that revolutionized gene delivery approaches. Since gene therapy using LVs attracted lots of attention to itself, we provided a brief review of LV structure and life-cycle along with methods for improving both LV production and transduction. Also, we mentioned some of their utilization in immunotherapy and gene therapy.

Tectonic 1 Is a Key Regulator of Cell Proliferation in Pancreatic Cancer

Pancreatic cancer is notoriously becoming one of the most devastating human cancers leading to death. However, clinical challenges still remain in diagnosis and treatment of this ticklish cancer. In the present study, the authors identified a new gene, Tectonic 1 (TCTN1), as a key regulator of cell proliferation in pancreatic cancer. Lentivirus-mediated short hairpin RNA (shRNA) was employed to knock down endogenous TCTN1 expression in PANC-1 pancreatic cancer cells. Knockdown of TCTN1 expression potently inhibited cell viability and proliferation, as determined by MTT and colony formation assays. Western blotting analysis also showed that knockdown of TCTN1 suppressed the expression of cdc2, while it induced that of p21 and p27. Flow cytometry analysis showed that depletion of TCTN1 in PANC-1 cells led to cell cycle arrest in the G2/M phase as well as apoptosis. Besides, depletion of TCTN1 led to the increase of Bax and cleavage of PARP-1, but the decrease of bcl2 by western blotting. The data indicate that TCTN1 is indispensable for pancreatic cancer cell proliferation, which provides a novel alternative to targeted therapy of pancreatic cancer and deserves further investigation.

Lentivirus-Mediated Knockdown of TCTN1 Inhibits Glioma Cell Proliferation

Tectonic-1, also named as TCTN1 or TECT1, which belongs to a family of signal-sequence-containing secreted and transmembrane proteins evolutionarily conserved among eukaryotes, was reported to be involved in central nervous system development and ciliogenesis. In this paper, we found that TCTN1 is extensively expressed in human glioma cell lines. To clarify the role of TCTN1 in glioma, we employed lentivirus-mediated short hairpin RNA to knock down TCTN1 expression in U251 and U87MG glioma cells. Knockdown of TCTN1 potently inhibited cell proliferation, as determined by MTT and colony formation assays. Cell cycle analysis showed depletion of TCTN1 led to both U251 and U87MG cells arrested in the G0/G1 phase. These data suggest TCTN1 is essential for glioma cell viability, and dysregulation of TCTN1 may play a key role in glioma tumorigenesis.

Polyglutamine (PolyQ) diseases: genetics to treatments

The polyglutamine (polyQ) diseases are a group of neurodegenerative disorders caused by expanded cytosine-adenine-guanine (CAG) repeats encoding a long polyQ tract in the respective proteins. To date, a total of nine polyQ disorders have been described: six spinocerebellar ataxias (SCA) types 1, 2, 6, 7, 17; Machado-Joseph disease (MJD/SCA3); Huntington's disease (HD); dentatorubral pallidoluysian atrophy (DRPLA); and spinal and bulbar muscular atrophy, X-linked 1 (SMAX1/SBMA). PolyQ diseases are characterized by the pathological expansion of CAG trinucleotide repeat in the translated region of unrelated genes. The translated polyQ is aggregated in the degenerated neurons leading to the dysfunction and degeneration of specific neuronal subpopulations. Although animal models of polyQ disease for understanding human pathology and accessing disease-modifying therapies in neurodegenerative diseases are available, there is neither a cure nor prevention for these diseases, and only symptomatic treatments for polyQ diseases currently exist. Long-term pharmacological treatment is so far disappointing, probably due to unwanted complications and decreasing drug efficacy. Cellular transplantation of stem cells may provide promising therapeutic avenues for restoration of the functions of degenerative and/or damaged neurons in polyQ diseases.

Recent advances in RNA interference therapeutics for CNS diseases

Over the last decade, RNA interference technology has shown therapeutic promise in rodent models of dominantly inherited brain diseases, including those caused by polyglutamine repeat expansions in the coding region of the affected gene. For some of these diseases, proof-of concept studies in model organisms have transitioned to safety testing in larger animal models, such as the nonhuman primate. Here, we review recent progress on RNA interference-based therapies in various model systems. We also highlight outstanding questions or concerns that have emerged as a result of an improved (and ever advancing) understanding of the technologies employed.

MiR-34a represses Numbl in murine neural progenitor cells and antagonizes neuronal differentiation

MicroRNA (miRNA) function is required for normal animal development, in particular in differentiation pathways from stem cell and precursor populations. In neurogenesis, it is becoming increasingly appreciated that miRNAs act at many stages to ensure proper progression. In this study we examined the role of miR-34a in neural progenitor cells (NPC) derived from murine embryonic cortex. We found that over-expression of miR-34a in NPC significantly reduced the neuron yield upon in vitro induction of differentiation. MiR-34a has several predicted targets in the Notch pathway, which operates to balance progenitor self-renewal and differentiation during cortical neurogenesis. We tested several Notch pathway players for regulation by miR-34a in undifferentiated NPC, and found that mRNA and protein levels of Numbl, a negative regulator of Notch signaling, as well as two downstream pro-neural genes usually blocked by Notch signaling, NeuroD1 and Mash1, were diminished, while Notch1 and Cbf1 transcripts were enhanced by miR-34a over-expression. Using a luciferase reporter assay, we verified the Numbl 3′-UTR as a direct miR-34a target. Correspondingly, knock-down of endogenous miR-34a resulted in increased Numbl, NeuroD1 and Mash1, and reduced Notch1 transcript levels. Together these results implicate Numbl as a physiologically relevant target of miR-34a in NPC, allowing for enhanced Notch signaling and inhibition of neuronal differentiation. This work extends our understanding of miR-34a-mediated control of cell differentiation from cancer to mammalian nervous system development.

Construction of permanently inducible miRNA-based expression vectors using site-specific recombinases

Background

RNA interference (RNAi) is a conserved gene silencing mechanism mediated by small inhibitory microRNAs (miRNAs).

Promoter-driven miRNA expression vectors have emerged as important tools for delivering natural or artificially designed miRNAs to eukaryotic cells and organisms. Such systems can be used to query the normal or pathogenic functions of natural miRNAs or messenger RNAs, or to therapeutically silence disease genes.

Results

As with any molecular cloning procedure, building miRNA-based expression constructs requires a time investment and some molecular biology skills. To improve efficiency and accelerate the construction process, we developed a method to rapidly generate miRNA expression vectors using recombinases instead of more traditional cut-and-paste molecular cloning techniques. In addition to streamlining the construction process, our cloning strategy provides vectors with added versatility. In our system, miRNAs can be constitutively expressed from the U6 promoter, or inducibly expressed by Cre recombinase. We also engineered a built-in mechanism to destroy the vector with Flp recombinase, if desired. Finally, to further simplify the construction process, we developed a software package that automates the prediction and design of optimal miRNA sequences using our system.

Conclusions

We designed and tested a modular system to rapidly clone miRNA expression cassettes. Our strategy reduces the hands-on time required to successfully generate effective constructs, and can be implemented in labs with minimal molecular cloning expertise. This versatile system provides options that permit constitutive or inducible miRNA expression, depending upon the needs of the end user. As such, it has utility for basic or translational applications.

Current prospects for RNA interference-based therapies

RNA interference (RNAi) is a powerful approach for reducing expression of endogenously expressed proteins. It is widely used for biological applications and is being harnessed to silence mRNAs encoding pathogenic proteins for therapy. Various methods - including delivering RNA oligonucleotides and expressing RNAi triggers from viral vectors - have been developed for successful RNAi in cell culture and in vivo. Recently, RNAi-based gene silencing approaches have been demonstrated in humans, and ongoing clinical trials hold promise for treating fatal disorders or providing alternatives to traditional small molecule therapies. Here we describe the broad range of approaches to achieve targeted gene silencing for therapy, discuss important considerations when developing RNAi triggers for use in humans, and review the current status of clinical trials.

RNA interference improves myopathic phenotypes in mice over-expressing FSHD region gene 1 (FRG1)

Muscular dystrophies, and other diseases of muscle, arise from recessive and dominant gene mutations. Gene replacement strategies may be beneficial for the former, while gene silencing approaches may provide treatment for the latter. In the last two decades, muscle-directed gene therapies were primarily focused on treating recessive disorders. This disparity at least partly arose because feasible mechanisms to silence dominant disease genes lagged behind gene replacement strategies. With the discovery of RNA interference (RNAi) and its subsequent development as a promising new gene silencing tool, the landscape has changed. In this study, our objective was to demonstrate proof-of-principle for RNAi therapy of a dominant myopathy in vivo. We tested the potential of adeno-associated viral (AAV)-delivered therapeutic microRNAs, targeting the human Facioscapulohumeral muscular dystrophy (FSHD) region gene 1 (FRG1), to correct myopathic features in mice expressing toxic levels of human FRG1 (FRG1(-high) mice). We found that FRG1 gene silencing improved muscle mass, strength, and histopathological abnormalities associated with muscular dystrophy in FRG1(-high) mice, thereby demonstrating therapeutic promise for treatment of dominantly inherited myopathies using RNAi. This approach potentially applies to as many as 29 different gene mutations responsible for myopathies inherited as dominant disorders.

Altering α-dystroglycan receptor affinity of LCMV pseudotyped lentivirus yields unique cell and tissue tropism

BACKGROUND

The envelope glycoprotein of lymphocytic choriomeningitis virus (LCMV) can efficiently pseudotype lentiviral vectors. Some strains of LCMV exploit high affinity interactions with α-dystroglycan (α-DG) to bind to cell surfaces and subsequently fuse in low pH endosomes. LCMV strains with low α-DG affinity utilize an unknown receptor and display unique tissue tropisms. We pseudotyped non-primate feline immunodeficiency virus (FIV) vectors using LCMV derived glycoproteins with high or low affinity to α-DG and evaluated their properties in vitro and in vivo.

METHODS

We pseudotyped FIV with the LCMV WE54 strain envelope glycoprotein and also engineered a point mutation in the WE54 envelope glycoprotein (L260F) to diminish α-DG affinity and direct binding to alternate receptors. We hypothesized that this change would alter in vivo tissue tropism and enhance gene transfer to neonatal animals.

RESULTS

In mice, hepatic α- and β-DG expression was greatest at the late gestational and neonatal time points. When displayed on the surface of the FIV lentivirus the WE54 L260F mutant glycoprotein bound weakly to immobilized α-DG. Additionally, LCMV WE54 pseudotyped FIV vector transduction was neutralized by pre-incubation with soluble α-DG, while the mutant glycoprotein pseudotyped vector was not. In vivo gene transfer in adult mice with either envelope yielded low transduction efficiencies in hepatocytes following intravenous delivery. In marked contrast, neonatal gene transfer with the LCMV envelopes, and notably with the FIV-L260F vector, conferred abundant liver and lower level cardiomyocyte transduction as detected by luciferase assays, bioluminescent imaging, and β-galactosidase staining.

CONCLUSIONS

These results suggest that a developmentally regulated receptor for LCMV is expressed abundantly in neonatal mice. LCMV pseudotyped vectors may have applications for neonatal gene transfer.

ABBREVIATIONS

Armstrong 53b (Arm53b); baculovirus Autographa californica GP64 (GP64); charge-coupled device (CCD); dystroglycan (DG); feline immunodeficiency virus (FIV); glycoprotein precursor (GP-C); firefly luciferase (Luc); lymphocytic choriomeningitis virus (LCMV); nuclear targeted β-galactosidase (ntLacZ); optical density (OD); PBS/0.1% (w/v) Tween-20 (PBST); relative light units (RLU); Rous sarcoma virus (RSV); transducing units per milliliter (TU/ml); vesicular stomatitis virus (VSV-G); wheat germ agglutinin (WGA); 50% reduction in binding (C50).

Enhanced gene expression conferred by stepwise modification of a nonprimate lentiviral vector

The practical application of gene transfer as a treatment for genetic diseases such as cystic fibrosis or hemophilia has been hindered, in part, by low efficiencies of vector delivery and transgene expression. We demonstrated that a feline immunodeficiency virus (FIV)-based lentiviral vector pseudotyped with the envelope glycoprotein from the baculovirus Autographa californica (GP64) efficiently transduces and persistently expresses a reporter gene in respiratory epithelium in the absence of agents that disrupt cellular tight junction integrity. GP64-pseudotyped FIV also efficiently transduced murine hepatocytes after tail vein delivery. To improve the FIV-based vector, we tested the contribution of a series of modifications to luciferase expression in vitro and in vivo. These modifications included the addition of spleen necrosis virus U5 (SNV U5) and mutation of the major splice donor and gag start codon located in the packaging region of the FIV transgene plasmid. After vector modification, we observed significantly enhanced expression of luciferase in respiratory epithelia after nasal application and in the liver after tail vein delivery. In addition, we observed significantly enhanced human factor VIII production after tail vein delivery. These sequential modifications provide an improved FIV lentivirus platform for gene therapy applications and may be applied to other retroviral vectors.

Human gene therapy vectors derived from feline lentiviruses

Lentiviral vectors are useful for gene transfer to dividing and nondividing cells. Feline immunodeficiency virus (FIV) vectors transduce most human cell types with good efficiency and may have advantages for clinical gene therapy applications. This article reviews significant progress in the development and refinement of FIV vector systems.

Lentivirus-mediated RNA interference in mammalian neurons

The ability to manipulate RNAi in cultured mammalian cells has provided scientists with a very powerful tool to influence gene expression. Neurons represent a cell type that initially displayed resistance to transduction by siRNAs or shRNA, when attempting to silence expression of endogenous genes. However, the development of lentiviral systems with that goal has facilitated the exogenous manipulation of RNAi in these postmitotic cells. Lentiviral-mediated RNAi experiments in cultured mammalian neurons can be designed to address a wide variety of biological questions or to test potential therapeutic hairpins before moving to treatment trials in vivo. We provide a practical approach to accomplish siRNA-mediated silencing of the disease-linked protein torsinA in primary neuronal cultures through the generation of lentiviral vectors expressing shRNAs.

Molecular characterization of feline immunodeficiency virus budding

Infection of domestic cats with feline immunodeficiency virus (FIV) is an important model system for studying human immunodeficiency virus type 1 (HIV-1) infection due to numerous similarities in pathogenesis induced by these two lentiviruses. However, many molecular aspects of FIV replication remain poorly understood. It is well established that retroviruses use short peptide motifs in Gag, known as late domains, to usurp cellular endosomal sorting machinery and promote virus release from infected cells. For example, the Pro-Thr/Ser-Ala-Pro [P(T/S)AP] motif of HIV-1 Gag interacts directly with Tsg101, a component of the endosomal sorting complex required for transport I (ESCRT-I). A Tyr-Pro-Asp-Leu (YPDL) motif in equine infectious anemia virus (EIAV), and a related sequence in HIV-1, bind the endosomal sorting factor Alix. In this study we sought to identify and characterize FIV late domain(s) and elucidate cellular machinery involved in FIV release. We determined that mutagenesis of a PSAP motif in FIV Gag, small interfering RNA-mediated knockdown of Tsg101 expression, and overexpression of a P(T/S)AP-binding fragment of Tsg101 (TSG-5') each inhibited FIV release. We also observed direct binding of FIV Gag peptides to Tsg101. In contrast, mutagenesis of a potential Alix-binding motif in FIV Gag did not affect FIV release. Similarly, expression of the HIV-1/EIAV Gag-binding domain of Alix (Alix-V) did not disrupt FIV budding, and FIV Gag peptides showed no affinity for Alix-V. Our data demonstrate that FIV relies predominantly on a Tsg101-binding PSAP motif in the C terminus of Gag to promote virus release in HeLa cells, and this budding mechanism is highly conserved in feline cells.

Inhibition of hepatitis B virus expression and replication by RNA interference

AIM: To study the RNA interference on hepatitis B virus (HBV) replication by a reverse transcription virus vector which can express short hairpin RNA inside cells.

METHODS: pSIREN vectors with inserted oligonucleotides targeting on reverse transcriptase (RT) regions of HBV genome were constructed. These plasmids were co-transfected with pHBV3.8 into Huh-7 cells. Viral antigens were measured by enzyme-linked immunosorbent assay (ELISA). HBV core particle DNA was measured and quantified by real-time fluorescence quantitative polymerase chain reaction (RFQ-PCR) and Southern blot. Viral RNA was analyzed by Northern blot.

RESULTS: Three RNA interfering targets were identified, and three corresponding retrovirus vectors, named 154i, 312i and 734i, were obtained. It was found that 312i markedly inhibited the expression of pHBV3.8, and the levels of HBsAg and HBeAg were 39% and 41% of those in the negative control group (P = 0.001, P = 0.000). RFQ-PCR showed that the level of HBV core particle DNA was significantly lower in 312i group than that in the negative control group (21.3% ± 1.1% vs 100.0% ± 10.6%, P = 0.0046). Southern and Northern blot demonstrated a lowest replication and transcription level of HBV in 312i group (10.5%, 12.0%).

CONCLUSION: A new RNAi system is identified in the RT regions of HBV genome, and the corresponding retrovirus vectors, which can remarkably inhibit the replication and expression of HBV, are also constructed.

RNA Interference: A Tool for Querying Nervous System Function and an Emerging Therapy

RNA interference (RNAi), a mediator of gene silencing, has swiftly become one of the most exciting and applicable biological discoveries. There has been rapid progress in identifying RNAi pathway components and elucidating the mechanisms of microRNA (miRNA) biogenesis and gene suppression. As a result, RNAi technologies have been successfully employed in a variety of systems as biological tools, and studies are underway to test the therapeutic utility of RNAi. In the span of several years, significant advances in the delivery of inhibitory RNAs in the nervous system have been made. We have glimpses into how endogenous miRNAs interface with neuronal development and function; in addition, RNAi has shown therapeutic efficacy in several mouse models of human neurological conditions. In this review, we summarize the current state-of-the-art of RNAi and its utility to neuroscientists.

Connecdenn, a novel DENN domain-containing protein of neuronal clathrin-coated vesicles functioning in synaptic vesicle endocytosis

Clathrin-coated vesicles (CCVs) are responsible for the endocytosis of multiple cargo, including synaptic vesicle membranes. We now describe a new CCV protein, termed connecdenn, that contains an N-terminal DENN (differentially expressed in neoplastic versus normal cells) domain, a poorly characterized protein module found in multiple proteins of unrelated function and a C-terminal peptide motif domain harboring three distinct motifs for binding the alpha-ear of the clathrin adaptor protein 2 (AP-2). Connecdenn coimmunoprecipitates and partially colocalizes with AP-2, and nuclear magnetic resonance and peptide competition studies reveal that all three alpha-ear-binding motifs contribute to AP-2 interactions. In addition, connecdenn contains multiple Src homology 3 (SH3) domain-binding motifs and coimmunoprecipitates with the synaptic SH3 domain proteins intersectin and endophilin A1. Interestingly, connecdenn is enriched on neuronal CCVs and is present in the presynaptic compartment of neurons. Moreover, connecdenn has a uniquely stable association with CCV membranes because it resists extraction with Tris and high-salt buffers, unlike most other CCV proteins, but it is not detected on purified synaptic vesicles. Together, these observations suggest that connecdenn functions on the endocytic limb of the synaptic vesicle cycle. Accordingly, disruption of connecdenn interactions with its binding partners through overexpression of the C-terminal peptide motif domain or knock down of connecdenn through lentiviral delivery of small hairpin RNA both lead to defects in synaptic vesicle endocytosis in cultured hippocampal neurons. Thus, we identified connecdenn as a component of the endocytic machinery functioning in synaptic vesicle endocytosis, providing the first evidence of a role for a DENN domain-containing protein in endocytosis.