scholarly journals High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones

2010 ◽  
Vol 84 (22) ◽  
pp. 11771-11780 ◽  
Author(s):  
Sanggu Kim ◽  
Namshin Kim ◽  
Angela P. Presson ◽  
Dong Sung An ◽  
Si Hua Mao ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Stem Cell ◽  
High Throughput ◽  
Integration Site ◽  
Genetic Diseases ◽  
Hematopoietic Stem ◽  
Vector Integration ◽  
Cell Clones ◽  
Clonality Analysis ◽  
Risk Of Cancer

ABSTRACT Retroviral vector-mediated gene therapy has been successfully used to correct genetic diseases. However, a number of studies have shown a subsequent risk of cancer development or aberrant clonal growths due to vector insertion near or within proto-oncogenes. Recent advances in the sequencing technology enable high-throughput clonality analysis via vector integration site (VIS) sequencing, which is particularly useful for studying complex polyclonal hematopoietic progenitor/stem cell (HPSC) repopulation. However, clonal repopulation analysis using the current methods is typically semiquantitative. Here, we present a novel system and standards for accurate clonality analysis using 454 pyrosequencing. We developed a bidirectional VIS PCR method to improve VIS detection by concurrently analyzing both the 5′ and the 3′ vector-host junctions and optimized the conditions for the quantitative VIS sequencing. The assay was validated by quantifying the relative frequencies of hundreds of repopulating HPSC clones in a nonhuman primate. The reliability and sensitivity of the assay were assessed using clone-specific real-time PCR. The majority of tested clones showed a strong correlation between the two methods. This assay permits high-throughput and sensitive assessment of clonal populations and hence will be useful for a broad range of gene therapy, stem cell, and cancer research applications.

Pre-Transplant Integration Site Diagnostics in Hematopoietic Stem Cell Gene Transfer.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 3581-3581
Author(s):  
Claudia R Ball ◽  
Sylvia Fessler ◽  
Daniela Belle ◽  
Manfred Schmidt ◽  
Christof von Kalle ◽  
...  
Keyword(s):  
Stem Cell ◽  
Ex Vivo ◽  
Integration Site ◽  
Hematopoietic Stem ◽  
Cell Clones ◽  
Integration Sites ◽  
Cell Gene ◽  
Stem Cell Gene

Abstract Abstract 3581 Poster Board III-518 We and others have previously shown that insertional activation of cellular genes caused by integrated retroviral vectors can lead to clonal dominance and malignant transformation. Pre-transplant diagnostics of vector flanking sequences and subsequent elimination of those clones that carry potentially dangerous integration sites prior to transplantation would dramatically improve the safety of clinical gene therapy regimens. Such a strategy requires efficient transduction of few or individual stem cells, their in vitro amplification and highly sensitive integration site determination before transplantation. To define optimal time points for transduction and ascertain the transplantability of ex vivo expanded murine stem cell clones, single CD45+Lin−Rho+SP cells isolated from bone marrow of male C57BL/6J (B6J) mice were cultivated for 8-10 days in the presence of IL11, SCF and Flt3-L. 10% of the sorted cells formed clones in vitro. In 28% ± 5% of these clones, the first division occurred during the first 48 hours after sorting, another 32% ± 8% divided up to 72 hours after sorting and additional 33% ± 7% up to 96 hours after sorting. 7% ± 4% had undergone their first division at a later time point. To examine the transplantability after ex vivo expansion, individual cell clones (containing 12 to >600 cells) were transplanted together with 105 carrier cells into lethally irradiated sex-mismatched syngeneic mice. The presence of donor-derived cells in peripheral blood of 20 transplanted mice was analyzed by Y-chromosome specific PCR. 55% of the ex vivo expanded clones contributed to post-transplant hematopoiesis. 25% of these clones exhibited long-term activity for >6 months after transplantation. Interestingly, only cell clones that had undergone their first division 48-96 hours after cell sorting contributed to long-term post-transplant hematopoiesis. For transduction, individual stem cell clones were spinoculated for 60 minutes with a GFP encoding lentiviral vector (MOI 100-5000). 5 days after transduction, 50% of cells generated by each clone were harvested, lysed and analyzed by LAM-PCR and integration site sequencing. After an additional 3 days, single clones were transplanted together with 105 carrier cells into lethally irradiated congeneic B6.SJL-PtprcaPepcb/BoyJ mice. Four weeks after transplantation, in 30% of these mice ≥0.4% CD45.1+ cells derived from single cell clones were detected in the peripheral blood. In 50% of these mice, the transduced clones contributed to myelopoiesis as well as lymphopoiesis for more than 24 weeks after transplantation, demonstrating that the longterm hematopoietic stem cell potential was retained after single cell marking and expansion. These results demonstrate that single stem cell gene transfer and subsequent expansion is possible to allow integration site determination. Long-term stem cells with defined lentiviral integration sites can be selected for transplantation. In summary, we provide proof of concept that pre-transplant diagnostics of integration sites is feasible to increase the safety of gene therapy by eliminating stem cell clones from transplants that carry unwanted integration sites. Disclosures: No relevant conflicts of interest to declare.

Clonal Analysis of Hematopoietic Stem Cells after Serial Transplantation of Animals Receiving MGMTP140K Gene Transduced Cells Following Chemotherapy.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1182-1182
Author(s):  
Stephanie Laufs ◽  
Ursula Sorg ◽  
Veronika Kleff ◽  
Laila Gao ◽  
Michael Flasshove ◽  
...  
Keyword(s):  
Stem Cells ◽  
Gene Therapy ◽  
Gene Transfer ◽  
Hematopoietic Stem Cells ◽  
Integration Site ◽  
Hematopoietic Stem ◽  
Vector Integration ◽  
Serial Transplantation ◽  
Selection Of

Abstract Gene transfer of the DNA repair protein O6-methylguanine-DNA-methyltransferase (MGMT) into hematopoietic stem cells has been shown to protect hematopoiesis from the toxic side effects of O6-guanine alkylating drugs such as BCNU, ACNU or temozolomide (TMZ). In addition, MGMT gene transfer allows efficient in vivo selection of transduced hematopoietic stem cells and enrichment of genetically corrected cells in the context of gene therapy for monogenetic diseases. We here have analysed the long-term effect of MGMT gene transfer on the hematopoietic stem cell compartment using an in vivo murine transplantation/gene therapy model and a retroviral vector carrying the gene for MGMTP140K, a mutant resistant to the wtMGMT-specific inhibitor O6-benzylguanine (BG). Serial transplants were performed and primary, secondary as well as tertiary recipients were treated with combined BG/ACNU, BG/BCNU or BG/TMZ chemotherapy at doses myeloablative in non-MGMT-protected hematopoiesis. Serial transplantation was performed with 1.8 – 3.0 x 106 mononuclear bone marrow cells and 2 to 3 animals were transplanted per primary or secondary animal. While initial gene transfer efficiency was low (1–5% of cells engrafted at week four) chemotherapy resulted in efficient selection of transduced cells in primary animals (70–90% transgene expression in peripheral blood). Secondary and tertiary recipients showed 40–80% transgene expression even before CTX. Efficient stem cell engraftment and protection from CTX was demonstrated in > 90% of secondary animals, while tertiary recipients clearly demonstrated compromised engraftment and a substantial number of animals did not survive CTX treatment. Retroviral vector integration site analysis to study the clonality of hematopoiesis of stem cells by ligation mediated PCR (LM-PCR) was performed in the serially transplanted mice. In three mice of the secondary transplantation cohort we detected 3, 0, and 6 clones, respectively. In three mice of the tertiary transplantation cohort 7, 2, and 2 clones, respectively, were found. Thus, an exhaustion of transduced hematopoiesis following regenerative stress by high dose chemotherapy was not evident. Of the total 20 detected clones one could not be mapped to the mouse genome, while the others could be blasted against the mouse genome (assembly 2004, http://genome.ucsc.edu/; >99.5% identity). It turned out that 5 of 8 integrations landed in RefSeq in the tertiary transplantation cohort, while 3 of 8 integrations occurred in RefSeq genes in the secondary transplantation cohort. This suggests that clones profit from the transcription machinery of their integration site. Thus, our LM-PCR results indicate that the multiclonality of hematopoiesis is conserved after serial transplants which may be considered a safety feature for drug-resistance gene therapy. Furthermore, vector integration in highly resistant stem cells is favored in actively transcribed genomic regions.

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

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.

Long-term hematopoietic stem cell gene therapy corrects neuromuscular manifestations in preclinical study of Pompe mice

2021 ◽  
Vol 132 (2) ◽  
pp. S107
Author(s):  
Niek P. van Til ◽  
Yildirim Dogan ◽  
Cecilia Barese ◽  
Zeenath Unnisa ◽  
Swaroopa Guda ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Stem Cell ◽  
Hematopoietic Stem Cell ◽  
Preclinical Study ◽  
Hematopoietic Stem ◽  
Cell Gene ◽  
Stem Cell Gene ◽  
Stem Cell Gene Therapy
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