On October 11, 2022 AVROBIO, Inc. (Nasdaq: AVRO), a leading clinical-stage gene therapy company working to free people from a lifetime of genetic disease, reported favorable data on the combined use of two state-of-the-art assays to evaluate the genotoxicity risk of integrating vectors used in hematopoietic stem cell (HSC) gene therapy prior to clinical use, at the 29th Annual Congress of the European Society of Gene & Cell Therapy (ESGCT), Oct. 11-14, 2022 in Edinburgh, Scotland (Press release, AVROBIO, OCT 11, 2022, View Source [SID1234621914]).
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In collaboration with Professor Axel Schambach, Ph.D., Institute of Experimental Hematology, Hannover Medical School, Germany, AVROBIO is pioneering the use of two advanced preclinical cell-based assays — in vitro immortalization (IVIM) assay and the novel surrogate assay for genotoxicity assessment (SAGA) — to evaluate viral vectors before they move into clinical programs. Together these assays are designed to assess which vectors are less likely to exhibit genotoxic behavior and monitor if these vectors activate proto-oncogenes (genes that may lead to cancer).
"Our work provides insight into the early molecular events of genotoxicity following HSC transduction with integrating vectors and presents a powerful machine-learning approach to prospectively estimate the genotoxicity risk of integrating vectors for gene therapy," said Professor Schambach, also associated with the Division of Hematology/Oncology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, whose work includes data on more than 30 commonly used vectors. "These assays enable preclinical risk assessment of gene therapy vectors, potentially paving the way for safer gene therapy vectors used in clinical trials."
AVROBIO uses these assays to inform vector selection during preclinical development. In addition, to date, AVROBIO has seen no cases of insertional oncogenesis in any of its clinical programs.
"Safety is at the forefront of our work at AVROBIO and incorporated in the development of our plato platform, which includes our advanced vector design, optimized for safety as well as transgene expression and protein uptake," said AVROBIO President and CEO Geoff MacKay. "Combining these assays helps assess vector genotoxicity risk early in preclinical development and further reaffirms that not all lentiviral vectors are designed the same."
IVIM/SAGA as screening tools during lentiviral vector selection
In its research, AVROBIO used the two assays in combination to determine the potential genotoxicity risk of six lentiviral vectors. Five of the vectors used the EF1 α short promoter (EFS), while the sixth vector used the modified enhancer/promoter of the murine myeloproliferative sarcoma virus, or MND, promoter. Vectors were compared to a non-transduced mock control and a positive genotoxic control, the non-SIN gamma-retroviral vector (RSF91).
The in vitro immortalization (IVIM) assay quantifies the risk of vector-induced cellular transformation. The technique assesses genotoxicity by determining how likely a vector is to insert near and activate proto-oncogenes, such as MECOM, and lead to an over-proliferation of cells. In this study, to quantify the risk of vector-induced cellular transformation, mouse hematopoietic stem and progenitor cell (HSPC) proliferation was monitored after transduction. IVIM determined that the five EFS vectors drove cell growth in a manner indistinguishable from non-transduced cells. The vector using the MND promoter, however, exhibited cell growth that was statistically significantly different from non-transduced cells and similar to the positive genotoxic control.
The second and newer assay assesses genotoxicity more directly. The novel surrogate assay for genotoxicity assessment (SAGA) relies on the observation that genotoxic vectors induce a unique gene expression signature that is linked to stemness and oncogenesis in mouse HSPCs. Machine learning algorithms developed from transcriptional data of known genotoxic vectors are used to estimate the transformational potential of candidate vectors. The SAGA assay can evaluate vectors with known genotoxic potential with an accuracy of 90.9%. In this study, SAGA data showed that the five vectors with EFS promoters were statistically distinct from the genotoxic positive control and therefore displayed lower genotoxic risk, whereas four of nine (44%) samples from cells transduced with a lentiviral vector containing an MND internal promoter had gene enrichment scores associated with insertional oncogenesis.
These findings enable the estimation of clinically translatable insertional oncogenesis risk of integrating vectors during preclinical development. AVROBIO uses the EFS promoter in its clinical programs.
The Hannover Medical School team working with Professor Schambach and Michael Rothe, Ph.D., has previously published their data in Molecular Therapy.