Molecular Therapy-Methods & Clinical Development最新文献

Lentiviral vector (LV)-based therapies employ the molecular machinery of HIV-1 to stably integrate therapeutic genes into patient cells for long-term disease correction. However, suboptimal expression of LV components in HEK293T-based production systems can limit titers and hinder clinical product development. Here, we identify protein kinase C (PKC) agonists as robust enhancers of LV production. PKC activation resulted in rapid transcription of LV genomic RNA and accelerated vector particle release in a manner that complemented the use of the histone deacetylase (HDAC) inhibitor, sodium butyrate. Stimulation of HEK293T cells strongly upregulated AP-1 transcription factor subunits independently of nuclear factor κB (NF-κB) pathway activation. Application of PKC agonists in LV production resulted in a ∼3-fold improvement in the titer of a chimeric antigen receptor (CAR)-LV. Furthermore, a ∼9-fold increase in titer was achieved when this induction method was combined with co-expression of an LV RNA-targeted U1 snRNA enhancer. Importantly, LV produced using PKC agonists had comparable particle-to-infectivity ratios and preserved T cell transduction efficiency. These findings suggest that incorporating PKC agonists into commercial LV manufacturing could considerably reduce the cost per patient dose of new LV-based gene therapies.

Viral copy-number (VCN) assay is a powerful, effective method to quantify toxicity, cellular kinetics, and durability of virus-modified cell therapy products. The qualification and validation of assay requires reference control. Traditionally, plasmids and cell lines are used as reference controls, but development and qualification of those controls require considerable time and resources. We propose a reference synthetic DNA fragment containing amplicons of woodchuck hepatitis virus posttranscriptional regulatory element (WPRE) and ribonuclease P protein subunit p30 (RPP30), connected by HindIII restriction enzyme cutting site, as a useful tool to qualify and validate duplex droplet digital PCR (ddPCR) assays for VCN. Using this hybrid amplicon, we qualified the duplex WPRE/RPP30 ddPCR assay by determining range of quantification, precision, bias, and robustness of the assay. The varying amount of input DNA showed upper limit, lower limit, and linearity of the assay. Coefficient of variation (CV) and % recovery showed assay precision and accuracy, respectively. Furthermore, the hybrid amplicon was used to determine assay robustness with potential conditions of variability. The hybrid amplicon was a comparable alternative to cell reference standards for validating VCN assay. In conclusion, WPRE-RPP30 hybrid amplicon can be used as a routine quality control measure to validate digital PCR assays.

Recent regulatory guidance now encourages the use of sequencing as an alternative adventitious agent testing assay to lengthy compendial in vivo assays used for cell line qualification. Most short-read sequencing assays, however, still require over a week to obtain a final test result since the sequencing must be completed before bioinformatic analysis can begin, which is still too long for some cell and gene therapy products that must be released as soon as possible to reach critically ill patients. Oxford Nanopore sequencing can address these issues, as it provides real-time basecalling and sequence alignment, which can reduce the overall assay time. Still, as with any sequencing platform, the abundance of background nucleic acid from the human or mammalian host can mask the signal from a low-level viral contaminant. To address this, we have developed a sensitive sample preparation workflow using concentration, nuclease treatment, and agnostic PCR methods to eliminate background signals and amplify viral contaminant reads, leading to a 3-log improvement in the limit of detection that is comparable to or better than short-read sequencing approaches. This approach will lead to more rapid and improved detection of viral contaminants in cell and gene therapy manufacturing.

Mucolipidosis IV (MLIV) is an autosomal-recessive pediatric disease that leads to motor and cognitive deficits and loss of vision. It is caused by loss of function of the lysosomal channel transient receptor potential mucolipin-1, TRPML1, and is associated with an early brain phenotype consisting of glial reactivity, hypomyelination, and lysosomal abnormalities. Although the field is approaching the first translationally relevant therapy, we currently lack a molecular signature of disease that can be used to detect therapeutic efficacy. Here, we analyzed 7,322 proteins in the plasma proteome from 17 MLIV patients and 37 controls and compared protein profiles with clinical measures of disease severity (motor function, muscle tone, and age). We found a decrease in neuronal proteins and an increase in muscle proteins in MLIV, consistent with neuronal dysfunction and muscle pathology observed in patients. Reduced synaptic proteins (e.g., GABARAP) best correlated with disease severity. Comparing the MLIV plasma proteome to the brain proteome from the MLIV mouse model identified shared alterations in 45 proteins, including upregulated proteins related to lysosomal function (e.g., ACTN2, GLB1) and downregulated proteins related to myelination (e.g., TPPP3, CNTN2). These data indicate that peripheral blood plasma protein signatures mirror changes found in the MLIV brain.

While lentiviral vectors have played a critical role in the emergence of gene-modified cell therapies, safety concerns remain regarding potential insertional mutagenesis. Regulatory authorities strongly recommend risk assessment and management of vector copy numbers (VCNs), integration profiles, and integration sites in the lentivirus-based cell and gene therapy products. However, accurately measuring these parameters remains a significant challenge due to the lack of standardized methodologies and VCN reference materials (RMs). Toward this challenge, we conducted an interlaboratory study on NIST candidate RMs for VCN measurements. The candidate RMs comprise five human genomic DNA samples or fixed cells from clonal Jurkat cell lines with defined VCNs ranging from 0 to 4. All 12 study participants were able to identify the VCN in the five blinded samples using quantitative PCR (qPCR), digital PCR (dPCR), or next generation sequencing (NGS) assays. Consensus value of VCN and integration sites in these candidate RMs were achieved. The fixed clonal VCN cells were also used to evaluate an emerging imaging-based technology called molecular combing. This interlaboratory assessment demonstrated the utility, commutability, and suitability of the NIST VCN candidate RMs for quality assurance and improved confidence in VCN, integration profile, and integration site measurements.

Natural killer (NK) cells are pivotal in immunosurveillance and hold great potential for immunotherapy due to their ability to target malignant cells. Their low risk of causing graft-versus-host disease (GvHD) post-allogenic transplantation underscores their potential as an off-the shelf cellular therapy tool. Advances in genetic engineering focus on improving NK targeting, persistence, and fitness. However, NK cells pose challenges for lentiviral transduction, which are clinically relevant and safe. In this study, we identified Poloxamer 407 (P407) as a novel transduction enhancer for rhesus macaque (RM) and human NK cells. We found that P407 significantly improved transduction efficiency, achieving up to 60% in expanded RM NK cells, without compromising cell viability or functionality. Additionally, P407 facilitated the expression of anti-CD20 chimeric antigen receptors (CARs) with or without interleukin (IL)-15. In a xenograft mouse model, CAR-IL15 NK cells demonstrated superior anti-tumor activity, and maintained higher clonal diversity tracked by genetic barcoding compared to CAR-NK cells lacking IL-15 in vivo. Additionally, in human NK cells, P407 combined with the TBK1/IKKε inhibitor, BX795, further improved lentivirus-mediated transduction. This study is the first to engineer NK cells from a clinically relevant rhesus macaque model in an adaptive cell therapy context and highlights P407's potential as a transduction enhancer.

Lipid nanoparticles (LNPs) can efficiently deliver nucleic acid therapeutics to a range of tissues, particularly hepatocytes to treat diseases of the liver. We initially investigated whether three LNPs with different ionizable lipids, previously validated in non-human primates (NHPs), could deliver functional GFP mRNA to human hepatocytes in chimeric NSG-PiZ and FRG mice. After intravenous delivery, GFP expression was observed throughout the livers but was restricted to mouse hepatocytes because the payload mRNA was not internalized by human hepatocytes. LNP transfection was also restricted to mouse hepatocytes in NSG-PiZ mice administered a different LNP containing the ionizable lipid SM-102. In vitro, primary human hepatocytes (PHHs) were transfected by LNPs containing lipids SM-102, LP01, or ALC0315 in the presence of normal mouse serum, but not chimeric NSG-PiZ serum. SM-102 LNP transfection of PHH was also inhibited by naive untransplanted NSG-PiZ serum. However, serum from NSG mice supported PHH transfection by SM-102 LNP. These results suggest that inhibitory factors in NSG-PiZ mouse serum are responsible for the lack of human hepatocyte transduction in chimeric mice. Finally, we found that LNPs displaying trivalent N-acetylgalactosamine (TriGalNAc), which targets them to the asialoglycoprotein receptor, can overcome species restriction, transfecting both mouse and human hepatocytes in chimeric NSG-PiZ mice.

Liver-humanized chimeric mice (PXB-mice) are widely utilized for predicting human pharmacokinetics (PK) and as human disease models. However, residual metabolic activity of mouse hepatocytes in chimeric mice can interfere with accurate human PK estimation. Lipid nanoparticle (LNP)-formulated small interfering RNA (siRNA) treatment makes it possible to eliminate the shortcomings of chimeras and create new models. Therefore, we aimed to create a new model in which siRNA for mouse cytochrome P450 oxidoreductase (Por) gene was encapsulated in LNP and administered to PXB-mice. We validated the siRNA-LNP system in PXB-mice, showing that a single intravenous injection of LNP-formulated mouse-specific siRNA against transthyretin (Ttr) knocked down Ttr expression in the liver and decreased plasma mouse TTR levels without affecting hepatic TTR expression and plasma human TTR levels. We produced mouse Por-specific siRNA with high in vitro silencing activity (siPOR(Mm)) and confirmed the efficient knockdown of Por expression in the livers of PXB-mice administered intravenously with LNP-encapsulated siPOR (siPOR(Mm)/LNP). siPOR(Mm)/LNP treatment suppressed 4'-hydroxywarfarin, making the S-warfarin PK profile in PXB-mice more similar to that in humans. Thus, mouse-specific siRNA-LNP is a simple system to control gene expression in the remaining mouse hepatocytes of PXB-mice and create more humanized and invaluable models based on PXB-mice.

Adeno-associated virus (AAV) vectors are widely used in gene therapy, particularly for liver-targeted treatments. However, predicting human-specific outcomes, such as transduction efficiency and hepatotoxicity, remains challenging. Reliable in vitro models are urgently needed to bridge the gap between preclinical studies and clinical applications. This study presents the first comparative evaluation of AAV transduction across multiple induced pluripotent stem cell (iPSC)-derived hepatocyte organoid donors, offering a novel platform for assessing vector performance in human liver models. The transduction efficiency and hepatotoxicity of eight AAV serotypes (AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV8, and AAV9) were tested in iPSC-derived liver organoids and hepatic cell lines (HepG2 and HepaRG). AAV6 and AAV8 exhibited the highest transduction efficiency in organoids, while AAV4 and AAV5 were the least effective. Transduction variability was observed across different donors and cell lines. Notably, no significant hepatotoxicity, measured by AST (aspartate aminotransferase) release and viability measurements, was observed, indicating that AAVs do not induce immediate liver damage in vitro. This study introduces iPSC-derived hepatocyte organoids as a novel and effective tool for predicting AAV transduction efficiency and safety, with potential to enhance the translation of gene therapies to clinical applications.