TALEN-mediated intron editing of HSPCs enables transgene expression restricted to the myeloid lineage

Gene therapy in hematopoietic stem and progenitor cells (HSPCs) shows great potential for the treatment of inborn metabolic diseases. Typical HSPC gene therapy approaches rely on constitutive promoters to express a therapeutic transgene, which is associated with multiple disadvantages. Here, we propose a novel promoterless intronic gene editing approach that triggers transgene expression only after cellular differentiation into the myeloid lineage. We integrated a splicing-competent eGFP cassette into the first intron of CD11b and observed expression of eGFP in the myeloid lineage but minimal to no expression in HSPCs or differentiated non-myeloid lineages. In vivo, edited HSPCs successfully engrafted in immunodeficient mice and displayed transgene expression in the myeloid compartment of multiple tissues. Using the same approach, we expressed alpha-L-iduronidase (IDUA), the defective enzyme in Mucopolysaccharidosis type I, and observed a 10-fold supraendogenous IDUA expression exclusively after myeloid differentiation. Edited cells efficiently populated bone marrow, blood, and spleen of immunodeficient mice, and retained the capacity to secrete IDUA ex vivo. Importantly, cells edited with the eGFP and IDUA transgenes were also found in the brain. This approach may unlock new therapeutic strategies for inborn metabolic and neurological diseases that require the delivery of therapeutics in brain.

Rescuing the cytolytic function of APDS1 patient T cells via TALEN-mediated PIK3CD gene correction

Gain-of-function mutations in the PIK3CD gene result in activated phosphoinositide 3-kinase δ syndrome type 1 (APDS1). This syndrome is a life-threatening combined immunodeficiency and today there are neither optimal nor long-term therapeutic solutions for APDS1 patients. Thus, new alternative treatments are highly needed. The aim of the present study is to explore one therapeutic avenue that consists of the correction of the PIK3CD gene through gene editing. Our proof-of-concept shows that TALEN-mediated gene correction of the mutated PIK3CD gene in APDS1 T cells results in normalized phospho-AKT levels in basal and activated conditions. Normalization of PI3K signaling was correlated to restored cytotoxic functions of edited CD8+ T cells. At the transcriptomic level, single-cell RNA sequencing revealed corrected signatures of CD8+ effector memory and CD8+ proliferating T cells. This proof-of-concept study paves the way for the future development of a gene therapy candidate to cure activated phosphoinositide 3-kinase δ syndrome type 1.

Abstract 3187: Improved anti-tumor immune functions of iPSC-derived NK cells with TGFβR2 knock-out and/or IL-15 knock-in by TALEN® editing for use alone or in combination with GPC3 Flex-NKTM bispecific antibody

Background: Induced Pluripotent Stem Cell (iPSC)-derived NK cells (iNK) offer an opportunity to generate unlimited homogenous NK cells as allogeneic off-the-shelf therapies. Interleukin-15 (IL-15) signaling enhances proliferation, persistence, cytotoxicity, and metabolic fitness of NK cells. Activation of TGF-β signaling suppresses anti-tumor functions of immune cells, including NK cells, in the tumor microenvironment (TME). In addition, previously, we have reported that our Flex-NKTM bispecific antibody that engages NK cells through NKp46 can enhance the cytotoxicity of the non-edited iNK cells. Therefore, we hypothesized that iNK cells with IL-15 knock-in (KI) and/or TGFβR2 knock-out (KO) could exhibit improved immune function and overcome the immunosuppressive TME. Furthermore, the activity of these edited universal iNK cells could be enhanced when combined with CYT-303, a Flex-NKTM bispecific antibody NK engager targeting GPC3 expressed on many solid tumors including hepatocellular carcinoma (HCC).

Methods: IL15 was knocked-in and/or TGFβR2 was knocked-out in iPSC using Cellectis TALEN® and the verified edited iPSC clones were differentiated and expanded into NK cells. The functional significance of these edits in iNKs were assessed in IL-15 and TGF-β dependent NK cell assays evaluating survival and proliferation, expression of activating receptors, as well as cytolysis of these iNK cells against HCC tumor cells. Cytotoxic activity of these edited cells was also tested in a serial killing assay with or without CYT-303 in the absence or presence of TGF-β.

Results: Compared to the non-edited iNK cells, iNKs with IL-15 KI can extend persistence in vitro in the absence of exogeneous cytokines. In the presence of TGF-β, the expression level of a number of NK cell activating receptors, such as NKG2D, DNAM-1, and NKp30, was decreased and lower cytotoxicity against HCC tumor cells was observed. However, this TGF-β-mediated immune suppression was reversed in TGFβR2 KO iNKs cells which also presented enhanced cytotoxicity against HCC cells. Furthermore, the anti-HCC cytotoxic activity of either single (IL-15 KI) or double edited (TGFβR2 KO and Il-15 KI) iNK cells were further enhanced by CYT-303, even in the presence of TGF-β. Serial killing assays against HCC tumor cells showed that the iNK cell dysfunction observed in later rounds of killing could still be reversed by the combination of these gene edits and CYT-303.

Conclusions: This work demonstrates that KI of IL-15 and KO of TGFβR2 is a promising strategy for TALEN®-engineered iNK cell therapies to overcome the immunosuppressive TME and mount a potent and persistent anti-tumor immune response. The data also provide a solid foundation for combining these edited iNK cells with CYT-303 to address the immunosuppressive TME towards a cure for HCC.

Citation Format: Liang Lin, Peng Gao, An-Ping Chen, Hao-Ming Chang, Preeti Ashok, David Zou, Marshall Chao Ma, Justin Eyquem, Alex Boyne, Alexandre Juillerat, Laurent Poirot, Philippe Duchateau, Armin Rath, Elisabetta Burchi, Daniel Teper, Antonio Arulanandam, Wei Li. Improved anti-tumor immune functions of iPSC-derived NK cells with TGFβR2 knock-out and/or IL-15 knock-in by TALEN® editing for use alone or in combination with GPC3 Flex-NKTM bispecific antibody [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3187.

Efficient multitool/multiplex gene engineering with TALE-BE

TALE base editors are a recent addition to the genome editing toolbox. These molecular tools are fusions of a transcription activator-like effector domain (TALE), split-DddA deaminase halves, and an uracil glycosylase inhibitor (UGI) that have the distinct ability to directly edit double strand DNA, converting a cytosine (C) to a thymine (T). To dissect the editing rules of TALE-BE, we combined the screening of dozens of TALE-BE targeting nuclear genomic loci with a medium/high throughput strategy based on precise knock-in of TALE-BE target site collections into the cell genome. This latter approach allowed us to gain in depth insight of the editing rules in cellulo, while excluding confounding factors such as epigenetic and microenvironmental differences among different genomic loci. Using the knowledge gained, we designed TALE-BE targeting CD52 and achieved very high frequency of gene knock-out (up to 80% of phenotypic CD52 knock out). We further demonstrated that TALE-BE generate only insignificant levels of Indels and byproducts. Finally, we combined two molecular tools, a TALE-BE and a TALEN, for multiplex genome engineering, generating high levels of double gene knock-out (∼75%) without creation of translocations between the two targeted sites.

Optimized two-step electroporation process to achieve efficient nonviral-mediated gene insertion into primary T cells

The development of gene editing technologies over the past years has allowed the precise and efficient insertion of transgenes into the genome of various cell types. Knock‐in approaches using homology‐directed repair and designer nucleases often rely on viral vectors, which can considerably impact the manufacturing cost and timeline of gene‐edited therapeutic products. An attractive alternative would be to use naked DNA as a repair template. However, such a strategy faces challenges such as cytotoxicity from double‐stranded DNA (dsDNA) to primary cells. Here, we sought to study the kinetics of transcription activator‐like effector nuclease (TALEN)‐mediated gene editing in primary T cells to improve nonviral gene knock‐in. Harnessing this knowledge, we developed a rapid and efficient gene insertion strategy based on either short single‐stranded oligonucleotides or large (2 Kb) linear naked dsDNA sequences. We demonstrated that a time‐controlled two‐step transfection protocol can substantially improve the efficiency of nonviral transgene integration in primary T cells. Using this approach, we achieved modification of up to ˜ 30% of T cells when inserting a chimeric antigen receptor (CAR) at the T‐cell receptor alpha constant region (TRAC) locus to generate ‘off‐the shelf’ CAR‐T cells.

Straightforward Generation of Ultrapure Off-the-Shelf Allogeneic CAR-T Cells

Here, we developed a straightforward methodology to generate TCRαβ negative (allogeneic) cells for CAR-T cell therapies. With an early and transient expression of an anti-CD3 CAR in the engineered donor T cells, we programmed these cells to self-eliminate the TCR+ cell population and obtained an ultrapure TCRαβ^– population (99–99.9%) at the end of the CAR-T production. This novel and easy-to-implement procedure preserves the production yield and cell fitness and has the potential to streamline the manufacturing of “off-the-shelf” CAR T-cell therapies.

Molecular signature of high yield (growth) influenza a virus reassortants prepared as candidate vaccine seeds

Background

Human influenza virus isolates generally grow poorly in embryonated chicken eggs. Hence, gene reassortment of influenza A wild type (wt) viruses is performed with a highly egg adapted donor virus, A/Puerto Rico/8/1934 (PR8), to provide the high yield reassortant (HYR) viral ‘seeds’ for vaccine production. HYR must contain the hemagglutinin (HA) and neuraminidase (NA) genes of wt virus and one to six ‘internal’ genes from PR8. Most studies of influenza wt and HYRs have focused on the HA gene. The main objective of this study is the identification of the molecular signature in all eight gene segments of influenza A HYR candidate vaccine seeds associated with high growth in ovo.

Methodology

The genomes of 14 wt parental viruses, 23 HYRs (5 H1N1; 2, 1976 H1N1-SOIV; 2, 2009 H1N1pdm; 2 H2N2 and 12 H3N2) and PR8 were sequenced using the high-throughput sequencing pipeline with big dye terminator chemistry.

Results

Silent and coding mutations were found in all internal genes derived from PR8 with the exception of the M gene. The M gene derived from PR8 was invariant in all 23 HYRs underlining the critical role of PR8 M in high yield phenotype. None of the wt virus derived internal genes had any silent change(s) except the PB1 gene in X-157. The highest number of recurrent silent and coding mutations was found in NS. With respect to the surface antigens, the majority of HYRs had coding mutations in HA; only 2 HYRs had coding mutations in NA.

Significance

In the era of application of reverse genetics to alter influenza A virus genomes, the mutations identified in the HYR gene segments associated with high growth in ovo may be of great practical benefit to modify PR8 and/or wt virus gene sequences for improved growth of vaccine ‘seed’ viruses.

Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse

Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV) produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA) receptor and non-structural protein 1 (NS1) interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA) variants obtained after 12 or 20–21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA) and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30) suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for studying IAV evolution to increased virulence in the mouse.

Examination of FMR1 transcript and protein levels among 74 premutation carriers

Fragile X-associated disorders are caused by a CGG trinucleotide repeat expansion in the 5'-untranslated region of the FMR1 gene. Expansion of the CGG trinucleotide repeats to >200 copies (that is, a full mutation) induces methylation of the FMR1 gene, with transcriptional silencing being the eventual outcome. Previous data have shown that FMR1 premutation carriers (individuals with 55-199 repeats) have increased FMR1 mRNA levels with decreased protein (fragile X mental retardation protein (FMRP)) levels. However, the point at which this translational inefficiency occurs, given the increased transcription mechanism, has not yet been explored and remains to be elucidated. We examined the repeat length group, FMR1 transcript and FMRP levels in 74 males with a wide range of repeat lengths using analysis of covariance to better characterize this association. Results showed that the mean FMRP level among carriers with 80-89 repeats was significantly higher than the mean levels among lower (54-79) and higher (90-120) premutation carriers, in spite of the increasing transcript level with repeat length. Taken together, these results suggest that the 80-89-repeat group may lead to different properties that increase the efficiency of translation compared with other premutation repeat size groups.

ATP-dependent calcium accumulation by non-mitochondrial organelles of axoplasm isolated from Myxicola giant axons

Axoplasm from freshly isolated Myxicola giant axons was mixed with small volumes of 'artificial axoplasm' containing 45Ca and either CaEGTA/EGTA or CaDTPA/DTPA buffers giving various nominal values of [Ca2+]. The axoplasm samples were centrifuged at 100 000 X g for 30 min to form a pellet and the percentage of 45Ca bound to the pellet was determined. The fraction of bound calcium rose with increasing values of [Ca2+] along an S-shaped curve. Carbonyl cyanide p-trifluoromethoxyphenylhydrazone (FCCP) was used to reveal the presence of mitochondrial Ca uptake. At physiological values of [Ca2+], around 100 nM, Ca uptake was insensitive to FCCP. As [Ca2+] was elevated, increasing sensitivity to FCCP was noted above [Ca2+] = 0.5 microM. At low values of [Ca2+], including the physiological range, Ca binding was significantly reduced by vanadate and quercetin, agents known to inhibit Ca uptake mediated by Ca2+-activated ATPase reactions. Inhibition of Ca binding by these agents was approximately 50% at physiological values of [Ca2+]. ATP depletion decreased the percentage of Ca binding by the pellet at physiological [Ca2+]. The results suggest that about 50% of the Ca buffering by particulate matter in axoplasm is via organelles requiring intact Ca2+-ATPase reaction at physiological values of [Ca2+].