Insertional Mutagenesis in Hematopoietic Cells: Lessons Learned from Adverse Events in Clinical Gene Therapy Trials

Abstract There is increasing evidence that insertional activation of proto-oncogenes by retroviral vectors is a significant safety issue that must be addressed before clinical gene therapy, particularly targeting hematopoietic stem and progenitor cells, can be further developed. The risk of insertional mutagenesis for replication-incompetent retroviral vectors has been assumed to be low until the occurence of T cell leukemias in children treated with HSC-directed gene therapy for X-SCID, and recent evidence that retroviral integration is more common in the promoter region of transcriptionally-active genes. The occurence of “common integration sites” in a particular gene also suggests a non-random insertion pattern, and/or immortalization or other change in the behavior of a clone harboring an insertion in these particular genes. We have previously reported a highly non-random occurence of 14 unique vector integrations in the first two introns of the MDS1/EVI1 proto-oncogene out of a total of 702 identified from myeloid cells of 9 rhesus macaques at least 6 months post-transplantion of retrovirally-transduced CD34+ cells.(Calmels et al, 2005). This same gene locus was found frequently activated by insertions in murine bone marrow cells immortalized in long-term in vitro culture after transduction with retroviral vectors.(Du et al Blood, 2005) To begin to investigate the factors contributing to this worrisome finding, particularly given the very recent report of a marked over-representation of MDS1/EVI1 insertions in a human clinical gene therapy trial for chronic granulomatous disease, we asked whether continued ex vivo expansion of transduced CD34+ cells prior to transplantation would further select for clones with insertions in MDS1/EVI1 or other proto-oncogenes. Rhesus CD34+ cells were transduced with the G1Na standard retroviral vector, identical to that used in the prior studies, using our standard 96 hour transduction protocol in the presence of Retronectin and SCF, FLT3L and thrombopoietin. At the end of transduction, all cells were continued in culture for an additional 7 days under the same culture conditions, and then reinfused into the donor animal following 1200 rads TBI. At 1 month post-transplant there were no CIS and no MDS1/EVI1 insertions identified. However, at 6 months post-transplantation 5 out of 27 (19%) of the unique insertions identified in granulocytes were within the first two introns of MDS1/EVI1, very significantly higher than the 2% of MDS1/EVI1 insertions (14 of 702) identified in animals that were transplanted with cells not subjected to additional ex vivo expansion.(p<.0001) One MDS1/EVI1 clone constituted 14% of overall sequences identified, and the 5 clones constituted 37% of total sequences identified. This strongly suggests that the over-representation of this locus in engrafting cells is due to a potent immortalizing signal provided by activation of the MDS1/EVI1 gene products by the stonger retroviral promoter/enhancer, and that the need for extended ex vivo culture of target cells may select for insertion events activating this locus. It also suggests that strategies involving prolonged ex vivo expansion or selection of transduced cells could increase the risk of gene therapy utilizing integrating vectors targeting primitive hematopoietic cells.

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The therapeutic potential of genome editing for β-thalassemia

F1000Research ◽

10.12688/f1000research.7087.1 ◽

2015 ◽

Vol 4 ◽

pp. 1431 ◽

Cited By ~ 3

Author(s):

Astrid Glaser ◽

Bradley McColl ◽

Jim Vadolas

Keyword(s):

Gene Therapy ◽

Genome Editing ◽

Insertional Mutagenesis ◽

Therapeutic Potential ◽

Allogeneic Bone Marrow Transplantation ◽

Lessons Learned ◽

Small Subset ◽

Allogeneic Bone ◽

Hematopoietic Stem ◽

Blood Disorder

The rapid advances in the field of genome editing using targeted endonucleases have called considerable attention to the potential of this technology for human gene therapy. Targeted correction of disease-causing mutations could ensure lifelong, tissue-specific expression of the relevant gene, thereby alleviating or resolving a specific disease phenotype. In this review, we aim to explore the potential of this technology for the therapy of β-thalassemia. This blood disorder is caused by mutations in the gene encoding the β-globin chain of hemoglobin, leading to severe anemia in affected patients. Curative allogeneic bone marrow transplantation is available only to a small subset of patients, leaving the majority of patients dependent on regular blood transfusions and iron chelation therapy. The transfer of gene-corrected autologous hematopoietic stem cells could provide a therapeutic alternative, as recent results from gene therapy trials using a lentiviral gene addition approach have demonstrated. Genome editing has the potential to further advance this approach as it eliminates the need for semi-randomly integrating viral vectors and their associated risk of insertional mutagenesis. In the following pages we will highlight the advantages and risks of genome editing compared to standard therapy for β-thalassemia and elaborate on lessons learned from recent gene therapy trials.

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Use of the in Vitro Immortalization Assay to Quantify the Impact of Integration Spectrum and Vector Design on Insertional Mutagenesis

Blood ◽

10.1182/blood.v118.21.3123.3123 ◽

2011 ◽

Vol 118 (21) ◽

pp. 3123-3123 ◽

Cited By ~ 1

Author(s):

Ute Modlich ◽

Julia Sürth ◽

Daniela Zychlinski ◽

Johann Meyer ◽

Christian Brendel ◽

...

Keyword(s):

Gene Therapy ◽

Insertional Mutagenesis ◽

Hepatitis Virus ◽

Hematopoietic Cells ◽

Human Leukemia ◽

Enhancer Activity ◽

Integration Pattern ◽

The Impact ◽

Selection Of

Abstract Abstract 3123 In gene therapy targeting hematopoietic cells, a quantitative assessment of the risk factors underlying insertional mutagenesis is required to assess the practical value of preventive actions. Emanating from an observation of the Copeland lab (Du et al., 2005) we developed an in vitro immortalization (IVIM) assay which determines the risk of transformation of murine bone marrow cells as a consequence of insertional upregulation of Evi1 or Prdm16. These functionally related genes encode master regulators of hematopoiesis which are involved in the pathogenesis of human leukemia and insertional transformation in human gene therapy. Using our standardized conditions, the assay can detect mutants arising with a low frequency (down to 1 in a million cells), based on their rescue and expansion upon replating. The genetic lesion associated with clonal transformation is easily identified, and we can quantify not only the incidence of mutants (number of cells required to form a mutant) but also their fitness (number of subclones obtained by replating). Using the IVIM assay, our published work has revealed the following: (1) relocating gammaretroviral enhancer-promoter sequences from the LTR to an internal position of a “self-inactivating” (SIN) vector reduces the fitness of mutants, as do mutations in transcription factor binding sites or insulators that reduce the enhancer activity; (2) cellular promoters located in SIN vectors, depending on their enhancer activity, may reduce the risk of transformation below the detection limit (>3 logs compared to standard gammaretroviral vectors); (3) the post-transcriptional regulatory element of the woodchuck hepatitis virus does not affect insertional transformation; and (4) the lentiviral integration pattern reduces the risk of insertional transformation by a factor of ∼3 compared to gammaretroviral vectors. In the meantime, the assay has been used to assess the transforming potential of new vectors developed to treat a variety of hematopoietic disorders, most notably X-SCID, X-CGD, WAS and globinopathies. Reproducibly we found that vectors containing cellular promoters reduced the risk of insertional transformation when compared to retroviral promoters, although not all cellular promoters appeared to be free of risk. The assay has also revealed major functional differences of various insulator elements, including synthetic ones designed to block enhancer-crosstalk. Testing a battery of 8 insulators that we obtained from collaborators or designed ourselves, we found that only a subset was potent enough to significantly reduce the transforming potential of a strong retroviral enhancer-promoter. Furthermore, we assessed the transforming potential of our new alpharetroviral SIN vectors (Suerth et al., JV 2010), modified to remove a residual TATA box of the LTR. When containing a retroviral internal promoter, alpharetroviral SIN vectors were ∼9-times and 3-times, respectively, less likely than the corresponding gammaretroviral and lentiviral constructs to induce strongly replicating clones. Mutants obtained with alpharetroviral SIN vector insertions in Evi1 were not only less frequent but also had a greatly reduced fitness compared to those induced by similarly designed gammaretroviral vectors. Alpharetroviral SIN vectors containing the human elongation factor 1 alpha promoter did not immortalize cells in this assay, as previously shown for gammaretroviral SIN vectors. Finally, we performed experiments to explore the mechanistic basis of the IVIM assay. Our data suggest that its principle is the selection of mutants that resist the differentiation-inducing effect of a myeloid growth factor cocktail. Therefore, variations of the cell culture conditions have a significant impact on the sensitivity of the assay, and potentially also on the spectrum of mutants that can be isolated. The established conditions typically select for upregulation of Evi1, Prdm16, or, more rarely observed, Ras -related genes. In summary, the IVIM assay quantifies the risk of insertional mutagenesis in gene therapy, related to vector sequences and integration pattern. It is specifically useful to assess the risk of insertional upregulation of Evi1 and Prdm16 via enhancer-mediated mechanisms, in myeloid progenitor cells. It thus serves as an animal replacement assay to screen for safety-enhancing vector modifications. Disclosures: Off Label Use: CliniMACS for selection of CD34+ hematopoietic cells.

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Initiation of a Pre-Clinical Gene Therapy Study in Non-Human Primates Using Lentivectors Targeting Hematopoietic Cells for Correction of Fabry Disease.

Blood ◽

10.1182/blood.v106.11.5542.5542 ◽

2005 ◽

Vol 106 (11) ◽

pp. 5542-5542 ◽

Cited By ~ 1

Author(s):

Jagdeep S. Walia ◽

Makoto Yoshimitsu ◽

Josh D. Silvertown ◽

Armando Poeppl ◽

Vanessa I. Rasaiah ◽

...

Keyword(s):

Gene Therapy ◽

Fabry Disease ◽

Peripheral Blood ◽

Rhesus Macaques ◽

Marker Gene ◽

Safety Information ◽

Hematopoietic Cells ◽

Hematopoietic Stem ◽

Cd34 Cells ◽

Clinical Gene Therapy

Abstract Fabry disease is a lysosomal storage disorder (LSD) due to low or absent levels of α-galactosidase A (α-gal A). This results in accumulation of substrate with terminal galactosyl residues such as globotriaosylceramide (Gb3) in lysosomes causing pathology in different organs. Previously, we have demonstrated correction of the deficiency in Fabry mice in numerous gene therapy studies targeting hematopoietic cells. Here we have initiated a pre-clinical gene therapy study in non-human primates (NHPs) targeting Fabry disease. Three rhesus macaques are housed in our animal facility and implantation of telemetric devices and vascular access ports have occurred. We have mobilized hematopoietic stem/progenitor cells from all three animals independently by treatment for 5 days with 10 μg/kg/day of recombinant human granulocyte colony stimulating factor (rhuG-CSF) and 200 μg/kg/day recombinant human stem cell factor (rhuSCF). On the 5th day of mobilization, all animals underwent leukapheresis. To be more clinically relevant, we are using a protocol with an unmodified, commercially available apheresis machine for the rhesus macaques, which can be used for humans of an equivalent weight. From each successful apheresis, we collected approximately 1 x109/kg mobilized peripheral blood mononuclear cells (MoPBMNCs). After collection of MoPBMNCs, we isolated CD34+ cells using an anti-human CD34 antibody (clone 12.8) with a recovery of approximately 15–20 x 106 CD34+ cells per kg body weight of the animal with >80% purity. Collected CD34+ cells are stored in liquid nitrogen. These cells will be prestimulated for 24 hours with huSCF, huFlt3L, huIL-6 and huTPO (kindly provided by Amgen) and will be transduced with a concentrated bicistronic lentivector (LV) that engineers co-expression of huα-gal A and huCD25, a cell surface marker for transduced cells. Our lab has recently shown overexpression of a rhesus form of CD25 in >80% of transduced rhesus BM CD34+ cells mediated by a LV, validating its candidacy as a marker gene. Transduced cells will then be transplanted autologously in the NHPs after myeloablation by irradiation (10Gy) or mild chemotherapy (fludarabine and cyclophosphamide). The irradiation protocol has been optimized and a special plexiglass chamber, with the capacity for inhalational and intravenous anesthesia as well as a space for a HEPA filter, has been prepared for the animal procedures. The transplanted animals will be followed for at least one year and outcomes will be assessed by full measurement of safety parameters, α-gal A activity in plasma and relevant organs along with the real-time PCR and LAM PCR on BM and peripheral blood cells for the persistence of LV. Gb3 levels will also be examined in different organs compared to pre-transplant levels in tissue biopsies. We expect that this preclinical study in NHPs will serve as a roadmap to clinical gene therapy of Fabry disease using LV and provide important safety information for the use of this promising gene delivery system.

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Practical gene delivery system suitable for clinical gene therapy

Nature Middle East ◽

10.1038/nmiddleeast.2010.238 ◽

2010 ◽

Author(s):

Abdulhakim Mahmoud

Keyword(s):

Gene Therapy ◽

Gene Delivery ◽

Delivery System ◽

Gene Delivery System ◽

Clinical Gene Therapy

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Long-term lymphoid progenitors independently sustain naïve T and NK cell production in humans

Nature Communications ◽

10.1038/s41467-021-21834-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Natalia Izotova ◽

Christine Rivat ◽

Cristina Baricordi ◽

Elena Blanco ◽

Danilo Pellin ◽

...

Keyword(s):

Stem Cells ◽

Gene Therapy ◽

Nk Cell ◽

Integration Site ◽

Hematopoietic Stem ◽

Cell Production ◽

Lymphoid Progenitors ◽

Clinical Gene Therapy ◽

Cancer Immunotherapies

AbstractOur mathematical model of integration site data in clinical gene therapy supported the existence of long-term lymphoid progenitors capable of surviving independently from hematopoietic stem cells. To date, no experimental setting has been available to validate this prediction. We here report evidence of a population of lymphoid progenitors capable of independently maintaining T and NK cell production for 15 years in humans. The gene therapy patients of this study lack vector-positive myeloid/B cells indicating absence of engineered stem cells but retain gene marking in both T and NK. Decades after treatment, we can still detect and analyse transduced naïve T cells whose production is likely maintained by a population of long-term lymphoid progenitors. By tracking insertional clonal markers overtime, we suggest that these progenitors can support both T and NK cell production. Identification of these long-term lymphoid progenitors could be utilised for the development of next generation gene- and cancer-immunotherapies.

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Gene Therapy in Hemophilia: Recent Advances

International Journal of Molecular Sciences ◽

10.3390/ijms22147647 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7647

Author(s):

E. Carlos Rodríguez-Merchán ◽

Juan Andres De Pablo-Moreno ◽

Antonio Liras

Keyword(s):

Gene Therapy ◽

Adverse Events ◽

Factor Viii ◽

Coagulation Factor ◽

Cost Savings ◽

Factor Ix ◽

Clotting Factors ◽

Advanced Therapies ◽

Potential Benefits

Hemophilia is a monogenic mutational disease affecting coagulation factor VIII or factor IX genes. The palliative treatment of choice is based on the use of safe and effective recombinant clotting factors. Advanced therapies will be curative, ensuring stable and durable concentrations of the defective circulating factor. Results have so far been encouraging in terms of levels and times of expression using mainly adeno-associated vectors. However, these therapies are associated with immunogenicity and hepatotoxicity. Optimizing the vector serotypes and the transgene (variants) will boost clotting efficacy, thus increasing the viability of these protocols. It is essential that both physicians and patients be informed about the potential benefits and risks of the new therapies, and a register of gene therapy patients be kept with information of the efficacy and long-term adverse events associated with the treatments administered. In the context of hemophilia, gene therapy may result in (particularly indirect) cost savings and in a more equitable allocation of treatments. In the case of hemophilia A, further research is needed into how to effectively package the large factor VIII gene into the vector; and in the case of hemophilia B, the priority should be to optimize both the vector serotype, reducing its immunogenicity and hepatotoxicity, and the transgene, boosting its clotting efficacy so as to minimize the amount of vector administered and decrease the incidence of adverse events without compromising the efficacy of the protein expressed.

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