A roadmap to safe, efficient, and stable lentivirus-mediated gene therapy with hematopoietic cell transplantation

Generation and Analysis of hTERT-RPE1 VPS54 Knock-Out and Rescued Cell Lines

The Golgi-associated retrograde protein (GARP) complex is proposed to tether endosome-derived transport vesicles, but the exact function and mechanism of GARP action are not completely understood. To uncover the GARP function in human cells, we employ CRISPR/Cas9 strategy and knock out (KO) the unique VPS54 subunit of the GARP complex. In this chapter, we describe the detailed method of generating CRISPR/Cas9-mediated VPS54-KO in hTERT-RPE1 cells, rescue of resulting KO cells with stable near-endogenous expression of myc-tagged VPS54, and validation of KO and rescued (KO-R) cells using Western blot and immunofluorescence approaches. This approach is helpful in uncovering new functions of the GARP and other vesicle tethering complexes.

Improving Lentiviral Transduction of CD34+ Hematopoietic Stem and Progenitor Cells

The delivery of therapeutic genes for treatment of inherited or infectious diseases frequently requires lentiviral transduction of CD34⁺ hematopoietic stem and progenitor cells (HSC). Optimized transduction protocols with a therapeutic goal aim to maximize the number of transduction-positive cells while limiting the vector copy number that reach each individual cell. Importantly, the transduced HSC should maintain their "stem-like" properties. Here, we analyzed LentiBOOST™ reagent, a membrane-sealing poloxamer, with respect to enhancing lentiviral transduction of CD34⁺ peripheral blood stem cells. We demonstrate that inclusion of LentiBOOST™ in a standard HSC transduction protocol yields high transduction efficiencies while preserving the ability of the transduced HSC to differentiate into various hematopoietic lineages. Thus, LentiBOOST™ reagent can significantly improve lentiviral CD34⁺ HSC transduction protocols with the potential to improve production of gene-modified cell products.

Engineering Hematopoietic Cells for Cancer Immunotherapy: Strategies to Address Safety and Toxicity Concerns

Advances in cancer immunotherapies utilizing engineered hematopoietic cells have recently generated significant clinical successes. Of great promise are immunotherapies based on chimeric antigen receptor-engineered T (CAR-T) cells that are targeted toward malignant cells expressing defined tumor-associated antigens. CAR-T cells harness the effector function of the adaptive arm of the immune system and redirect it against cancer cells, overcoming the major challenges of immunotherapy, such as breaking tolerance to self-antigens and beating cancer immune system-evasion mechanisms. In early clinical trials, CAR-T cell-based therapies achieved complete and durable responses in a significant proportion of patients. Despite clinical successes and given the side effect profiles of immunotherapies based on engineered cells, potential concerns with the safety and toxicity of various therapeutic modalities remain. We discuss the concerns associated with the safety and stability of the gene delivery vehicles for cell engineering and with toxicities due to off-target and on-target, off-tumor effector functions of the engineered cells. We then overview the various strategies aimed at improving the safety of and resolving toxicities associated with cell-based immunotherapies. Integrating failsafe switches based on different suicide gene therapy systems into engineered cells engenders promising strategies toward ensuring the safety of cancer immunotherapies in the clinic.

Genetic Modification of the Lung Directed Toward Treatment of Human Disease

Genetic modification therapy is a promising therapeutic strategy for many diseases of the lung intractable to other treatments. Lung gene therapy has been the subject of numerous preclinical animal experiments and human clinical trials, for targets including genetic diseases such as cystic fibrosis and α1-antitrypsin deficiency, complex disorders such as asthma, allergy, and lung cancer, infections such as respiratory syncytial virus (RSV) and Pseudomonas, as well as pulmonary arterial hypertension, transplant rejection, and lung injury. A variety of viral and non-viral vectors have been employed to overcome the many physical barriers to gene transfer imposed by lung anatomy and natural defenses. Beyond the treatment of lung diseases, the lung has the potential to be used as a metabolic factory for generating proteins for delivery to the circulation for treatment of systemic diseases. Although much has been learned through a myriad of experiments about the development of genetic modification of the lung, more work is still needed to improve the delivery vehicles and to overcome challenges such as entry barriers, persistent expression, specific cell targeting, and circumventing host anti-vector responses.

Interferon induced transmembrane protein 3 regulates the growth and invasion of human lung adenocarcinoma

Background

Interferon induced transmembrane protein 3 (IFITM3) plays an important role in the tumorigenesis and progression of multiple cancers. This study investigated the expression and function of IFITM3 in human lung adenocarcinoma.

Methods

Fifty human lung adenocarcinoma tissues were collected. IFITM3 expression was assessed by immunohistochemical staining. The clinicopathologic characteristics of all patients were analyzed.

Results

IFITM3 was mainly detected in the cytoplasm of advanced cancer tissues and its expression was correlated with tumor malignancy grade. Knockdown of IFITM3 in vitro markedly inhibited the proliferation and invasion of lung adenocarcinoma cells.

Conclusion

IFITM3 represents a potential therapeutic target for the treatment of lung adenocarcinoma.

Construction of a recombinant lentiviral vector expressing shRNA targeting KDM5C gene and its effect on proliferation and invasion of hepatocellular carcinoma HepG2 cells

AIM

To screen specific short hairpin RNA (shRNA) targeting the KDM5C gene, generate a recombinant lentiviral vector carrying KDM5C specific shRNA (Lv-shKDM5C), and investigate its effect on the proliferation and invasion of hepatocellular carcinoma HepG2 cells and lncRNA GAS5 expression.

METHODS

Three pairs of shRNA fragments against the KDM5C (shKDM5C) gene and one negative control shRNA (shNC) were designed and synthesized, and a recombinant lentiviral vector was constructed using subcloning techniques. Subsequently the recombinant lentiviruses were packaged into 293T cells by co-transfection with four plasmids. The titer of virus was detected according to the expression of enhanced green fluoreseen protein (GFP). The packaged lentiviruses were transfected into HepG2 cells, and the mRNA and protein expression of KDM5C was detected by qRT-PCR and Western blot, respectively. The optimal recombinant lentiviral vector for KDM5C silencing was screened. The proliferation and invasion of HepG2 cells were detected by MTT and wound healing assay, respectively.

RESULTS

Three recombinant lentiviruses were constructed successfully. The titers of Lv-shKDM5C-1, Lv-shKDM5C-2 and Lv-shKDM5C-3 were 4.95 × 10⁸ TU/mL, 3.46 × 10⁸ TU/mL and 3.08 × 10⁸ TU/mL, respectively. HepG2 cells had higher KDM5C expression than normal hepatic cells (L02 cells; P < 0.05). Compared to non-infected and negative control cells, the mRNA and protein expression levels of KDM5C were significantly inhibited in HepG2 cells transfected with Lv-shKDM5C, with Lv-shKDM5C-3 having the highest interference efficiency. The cell proliferation was significantly decreased at 48 h and 72 h (P < 0.05 for both) and the wound closure rate was significantly decreased at 48 h after Lv-shKDM5C-3 transfection, compared to the Lv-shNC group (P < 0.05). Moreover, Lv-shKDM5C-3 transfection significantly increased the mRNA level of lncRNA GAS5 (P < 0.05).

CONCLUSION

A recombinant lentiviral vector expressing shRNA targeting the human KDM5C gene has been successfully constructed, and it can effectively inhibit the proliferation and invasion of HepG2 cells. Inhibition of KDM5C expression increases the expression of lncRNA GAS5 in HepG2 cells.

Good Manufacturing Practices (GMP) manufacturing of advanced therapy medicinal products: a novel tailored model for optimizing performance and estimating costs

BACKGROUND AIMS

Advanced therapy medicinal products (ATMP) have gained considerable attention in academia due to their therapeutic potential. Good Manufacturing Practice (GMP) principles ensure the quality and sterility of manufacturing these products. We developed a model for estimating the manufacturing costs of cell therapy products and optimizing the performance of academic GMP-facilities.

METHODS

The "Clean-Room Technology Assessment Technique" (CTAT) was tested prospectively in the GMP facility of BCRT, Berlin, Germany, then retrospectively in the GMP facility of the University of California-Davis, California, USA. CTAT is a two-level model: level one identifies operational (core) processes and measures their fixed costs; level two identifies production (supporting) processes and measures their variable costs. The model comprises several tools to measure and optimize performance of these processes. Manufacturing costs were itemized using adjusted micro-costing system.

RESULTS

CTAT identified GMP activities with strong correlation to the manufacturing process of cell-based products. Building best practice standards allowed for performance improvement and elimination of human errors. The model also demonstrated the unidirectional dependencies that may exist among the core GMP activities. When compared to traditional business models, the CTAT assessment resulted in a more accurate allocation of annual expenses. The estimated expenses were used to set a fee structure for both GMP facilities. A mathematical equation was also developed to provide the final product cost.

CONCLUSIONS

CTAT can be a useful tool in estimating accurate costs for the ATMPs manufactured in an optimized GMP process. These estimates are useful when analyzing the cost-effectiveness of these novel interventions.

Cell fate control gene therapy based on engineered variants of human deoxycytidine kinase

The safety of cell therapy applications can be enhanced by the introduction of Cell Fate Control (CFC) elements, which encode pharmacologically controlled cellular suicide switches. CFC Gene Therapy (CFCGT) offers the possibility of establishing control over gene-modified cells (GMCs) with regards to their proliferation, differentiation, or function. However, enzymes commonly employed in these approaches often possess poor kinetics and high immunogenicity. We describe a novel CFCGT system based on engineered variants of human deoxyCytidine Kinase (dCK) that overcomes limitations of current modalities. Mutants of dCK with rationally designed active sites that make them thymidine-activating were stably introduced into cells by recombinant lentiviral vectors (LVs). Transduced cells maintained growth kinetics and function. These dCK mutants efficiently activate bromovinyl-deoxyuridine (BVdU), L-deoxythymidine (LdT), and L-deoxyuridine (LdU), which are otherwise not toxic to wild-type cells. We show that mutant dCK-expressing Jurkat, Molt-4, and U87mg cells could be efficiently eliminated in vitro and in xenogeneic leukemia and tumor models in vivo. We also describe a fusion construct of the thymidine-activating dCK to the cytoplasmic tail-truncated LNGFR molecule and applications to in vivo eradication of primary human T cells. This novel CFCGT system offers unique plasticity with respect to the wide range of prodrugs it can potentiate, and can be used as a reliable safety switch in cell and gene therapy.

Transient proteasome inhibition as a strategy to enhance lentiviral transduction of hematopoietic CD34(+) cells and T lymphocytes: implications for the use of low viral doses and large-size vectors

The proteasome system restricts lentiviral transduction of stem cells. We exploited proteasome inhibition as a strategy to enhance transduction of both hematopoietic stem cells (HSC) and T lymphocytes with low dose or large-size lentiviral vectors (LV). HSC showed higher transduction efficiency if transiently exposed to proteasome inhibitor MG132 (41.8% vs 10.7%, p<0.0001). Treatment with MG132 (0.5 μM) retained its beneficial effect with 3 different LV of increasing size up to 10.9 Kb (p<0.01). We extended, for the first time, the application of proteasome inhibition to the transduction of T lymphocytes. A transient exposure to MG132 significantly improved lentiviral T-cell transduction. The mean percentage of transduced T cells progressively increased from 13.5% of untreated cells, to 21% (p=0.3), 30% (p=0.03) and 37% (p=0.01) of T lymphocytes that were pre-treated with MG132 at 0.1, 0.5 and 1 μM, respectively. MG132 did not affect viability or functionality of HSC or T cells, nor significantly increased the number of integrated vector copies. Transient proteasome inhibition appears as a new procedure to safely enhance lentiviral transduction of HSC and T lymphocytes with low viral doses. This approach could be useful in settings where the use of large size vectors may impair optimal viral production.

Lentiviral vectors: their molecular design, safety, and use in laboratory and preclinical research

Lentiviral vectors have been successfully used in the clinic and they are increasingly being used for nonclinical applications. They are capable of stably transducing a broad range of mammalian cell types, including nondividing cells, with high efficiency. This review summarizes the evolving molecular design of lentiviral vectors, describing how they have improved since their first description. Lentiviral vector safety and issues surrounding genotoxicity are discussed. Examples of successful application of lentiviral vectors in laboratory and preclinical research are described. These include functional genomics, target validation, protein manufacturing, in vivo imaging, transgenic animals, and stem cell research.

COS-1 cells as packaging host for production of lentiviruses

We present a protocol for in vitro production of recombinant lentiviruses using COS-1 African green monkey kidney epithelial cells and HEK293T human embryonic kidney epithelial cells as packaging cells. COS-1 and HEK293T express SV40 large T antigen, amplifying transfected circular plasmids harboring SV40 replication origin. Support protocols for evaluation of transfection efficiency by in situ β-galactosidase enzyme activity assay and titer of infection-capable virions are also provided. Advantages of using COS-1 packaging cells over the standard HEK293T cells for contamination-sensitive applications or automated processing are discussed.

Construction of a lentiviral vector carrying an MCFP shRNA and generation of a HepG2 cell line stably transfected with this vector

AIM: To construct a lentiviral vector carrying a short hairpin RNA (shRNA) targeting the mitochondrial carrier functional protein SLC25A40 (MCFP) gene and to detect the silencing effect of the vector in HepG2 cell line.

METHODS: A double-stranded shRNA targeting the MCFP gene was designed, synthesized and cloned into the pSiCoR vector. The resulting lentiviral vector containing the MCFP shRNA was named pSiCoR-MCFP. HepG2 cells were transfected with the pSiCoR-MCFP lentivirus to obtain a cell line stably expressing the MCFP shRNA. After transfection, the mRNA and protein expression of MCFP in HepG2 cells was detected by RT-PCR and Western blot, respectively.

RESULTS: A lentiviral vector carrying an shRNA targeting the MCFP gene was successfully constructed and a HepG2 cell line stably transfected with the vector was established. The recombinant lentivirus and control lentivirus harvested from 293 cells had a titer of 1.78 × 10¹⁰ pfu/L and 1.45 × 10¹⁰ pfu/L, respectively. RT-PCR and Western blot analyses confirmed that the expression of MCFP was down-regulated in HepG2 cell line stably transfected with the recombinant vector (both P < 0.001).

CONCLUSION: A lentiviral vector carrying an shRNA targeting the MCFP gene was successfully constructed and a HepG2 cell line stably transfected with the vector was established.

Autologous transplantation of lentivector/acid ceramidase-transduced hematopoietic cells in nonhuman primates

Farber disease is a rare lysosomal storage disorder (LSD) that manifests due to acid ceramidase (AC) deficiencies and ceramide accumulation. We present a preclinical gene therapy study for Farber disease employing a lentiviral vector (LV-huAC/huCD25) in three enzymatically normal nonhuman primates. Autologous, mobilized peripheral blood (PB) cells were transduced and infused into fully myelo-ablated recipients with tracking for at least 1 year. Outcomes were assessed by measuring the AC specific activity, ceramide levels, vector persistence/integration, and safety parameters. We observed no hematological, biochemical, radiological, or pathological abnormalities. Hematological recovery occurred by approximately 3 weeks. Vector persistence was observed in PB and bone marrow (BM) cells by qualitative and quantitative PCR. We did not observe any clonal proliferation of PB and BM cells. Importantly, AC-specific activity was detected above normal levels in PB and BM cells analyzed post-transplantation and in spleens and livers at the endpoint of the study. Decreases of ceramide in PB cells as well as in spleen and liver tissues were seen. We expect that this study will provide a roadmap for implementation of clinical gene therapy protocols targeting hematopoietic cells for Farber disease and other LSDs.

Mesenchymal stromal cells for graft-versus-host disease

Mesenchymal stromal cells (MSCs) have been shown to mediate immune responses in vitro and in vivo. These observations have led to clinical trials of MSC administration to ameliorate acute graft-versus-host disease (GVHD), the most serious complication arising after allogeneic hematopoietic cell transplantation. Clinical data suggest a benefit in approximately two-thirds of patients with steroid-resistant acute GVHD. Preliminary studies have been reported on the use of MSCs to treat de novo acute GVHD, for prophylaxis of the condition, and more recently, in the management of chronic GVHD. Although preclinical data inferred a possible role of MSCs in affecting GVHD mechanisms, more robust animal models became available only after numerous clinical trials with these cells had been undertaken. Further clinical trials, the development of more appropriate animal models and an effective means of tracking and imaging the introduced cells in real time in patients, are required to better define their role in this important area of medicine.

Creating higher titer lentivirus with caffeine

The use of lentiviral vectors extends from the laboratory, where they are used for basic studies in virology and as gene transfer vectors gene delivery, to the clinic, where clinical trials using these vectors for gene therapy are currently underway. Lentiviral vectors are useful for gene transfer because they have a large cloning capacity and a broad tropism. Although procedures for lentiviral vector production have been standardized, simple methods to create higher titer virus during production would have extensive and important applications for both research and clinical use. Here we present a simple and inexpensive method to increase the titer by 3- to 8-fold for both integration-competent lentivirus and integration-deficient lentivirus. This is achieved during standard lentiviral production by the addition of caffeine to a final concentration of 2-4 mM. We find that sodium butyrate, a histone deacetylase inhibitor shown previously to increase viral titer, works only ∼50% as well as caffeine. We also show that the DNA-PKcs (DNA-dependent protein kinase catalytic subunit) inhibitor NU7026 can also increase viral titer, but that the combination of caffeine and NU7026 is not more effective than caffeine alone. We show that the time course of caffeine treatment is important in achieving a higher titer virus, and is most effective when caffeine is present from 17 to 41 hr posttransfection. Last, although caffeine increases lentiviral vector titer, it has the opposite effect on the titer of adeno-associated virus type 2 vector. Together, these results provide a novel, simple, and inexpensive way to significantly increase the titer of lentiviral vectors.

Platelets as delivery systems for disease treatments

Platelets are small, anucleate, discoid shaped blood cells that play a fundamental role in hemostasis. Platelets contain a large number of biologically active molecules within cytoplasmic granules that are critical to normal platelet function. Because platelets circulate in blood through out the body, release biological molecules and mediators on demand and participate in hemostasis as well as many other pathophysiologic processes, targeting expression of proteins of interest to platelets and utilizing platelets as delivery systems for disease treatment would be a logical approach. This paper reviews the genetic therapy for inherited bleeding disorders utilizing platelets as delivery system, with a particular focus on platelet-derived FVIII for hemophilia A treatment.

Combination stem cell therapy for heart failure

Patients with congestive heart failure (CHF) that are not eligible for transplantation have limited therapeutic options. Stem cell therapy such as autologous bone marrow, mobilized peripheral blood, or purified cells thereof has been used clinically since 2001. To date over 1000 patients have received cellular therapy as part of randomized trials, with the general consensus being that a moderate but statistically significant benefit occurs. Therefore, one of the important next steps in the field is optimization. In this paper we discuss three ways to approach this issue: a) increasing stem cell migration to the heart; b) augmenting stem cell activity; and c) combining existing stem cell therapies to recapitulate a "therapeutic niche". We conclude by describing a case report of a heart failure patient treated with a combination stem cell protocol in an attempt to augment beneficial aspects of cord blood CD34 cells and mesenchymal-like stem cells.

Construction and identification of a lentiviral vector for RNA interference of the Cdx2 gene

AIM: To construct a lentiviral vector for RNA interference (RNAi) of the caudal-related homeobox 2 (Cdx2) gene.

METHODS: A pair of complementary small hairpin RNA (shRNA) oligonucleotides targeting the Cdx2 gene were designed, synthesized, annealed and inserted into linearized pLentiLox3.7 vector. The recombinant plasmid was identified by double restriction digestion with Xba I/Not I and DNA sequencing. The recombinant plasmid and a lentivirus packaging mix were co-transfected into 293T cells to obtain packaged lentivirus particles. Viral titer was then determined.

RESULTS: Double restriction digestion analysis and DNA sequencing showed that the shRNA sequence was successfully inserted into the pLentiLox3.7 vector. The recombinant lentiviral vector harboring shRNA targeting the Cdx2 gene was successfully transfected into 293T cells. The recombinant lentivirus harvested from 293T cells had a titer of 5×107 TU/mL.

CONCLUSION: A lentiviral shRNA expression vector targeting the Cdx2 gene is successfully constructed and can be used for further study of the role of the Cdx2 gene in the pathogenesis of gastric cancer.

Enhancement of myogenic and muscle repair capacities of human adipose-derived stem cells with forced expression of MyoD

Muscle disorders such as Duchenne muscular dystrophy (DMD) still need effective treatments, and mesenchymal stem cells (MSCs) may constitute an attractive cell therapy alternative because they are multipotent and accessible in adult tissues. We have previously shown that human multipotent adipose-derived stem (hMADS) cells were able to restore dystrophin expression in the mdx mouse. The goal of this work was to improve the myogenic potential of hMADS cells and assess the impact on muscle repair. Forced expression of MyoD in vitro strongly induced myogenic differentiation while the adipogenic differentiation was inhibited. Moreover, MyoD-expressing hMADS cells had the capacity to fuse with DMD myoblasts and to restore dystrophin expression. Importantly, transplantation of these modified hMADS cells into injured muscles of immunodepressed Rag2(-/-)gammaC(-/-) mice resulted in a substantial increase in the number of hMADS cell-derived fibers. Our approach combined the easy access of MSCs from adipose tissue, the highly efficient lentiviral transduction of these cells, and the specific improvement of myogenic differentiation through the forced expression of MyoD. Altogether our results highlight the capacity of modified hMADS cells to contribute to muscle repair and their potential to deliver a repairing gene to dystrophic muscles.

Advantages of COS-1 monkey kidney epithelial cells as packaging host for small-volume production of high-quality recombinant lentiviruses

The HEK293T human embryonic kidney cells have been used widely as a packaging host for transfection-based production of recombinant lentiviruses. The present study describes advantages of using COS-1 African green monkey kidney cells versus HEK293T cells as a packaging host for small-volume production of high-quality recombinant lentiviruses. The particle performance index, defined as the ratio of infection-competent viral particles to the total number of particles, was three- to four-fold greater in transfection supernatants generated using COS-1 cells than that generated using HEK293T cells. Adhesion of HEK293T cells to the cell culture-treated plastic surface was weak, causing significant HEK293T cell contamination in the transfection supernatants produced by laboratory automation using the 96-well cell culture plates. In contrast, COS-1 cells adhered strongly to the plastic surface, and cell contamination was not detected in the transfection supernatants. These results suggest that COS-1 cells may be a useful alternative packaging host for use for automated generation of large numbers of high-quality lentivirus reagents, particularly because they eliminate the need for additional purification steps to remove viral particles from cell culture supernatant.