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Systemic epigenetic response to recombinant lentiviral vectors independent of proviral integration.

Aranyi T, Stockholm D, Yao R, Poinsignon C, Wiart T, Corre G, Touleimat N, Tost J, Galy A, Paldi A - Epigenetics Chromatin (2016)

Bottom Line: The effects of LV on target cells are expected to be limited to gene delivery.This effect required cellular entry of the viral particle in the cells but not the genomic integration of the vector cassette.Some LV preparations induced only mild sporadic changes while others had strong effects suggesting that LV batch heterogeneity may be related to the extent of the epigenetic response.

View Article: PubMed Central - PubMed

Affiliation: Université Evry Val d'Essonne, UMRS_951, Genethon, 91002 Evry, France.

ABSTRACT

Background: Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cells respond to functional LVs as well as several types of non-integrating LVs by genome-wide DNA methylation changes.

Results: A new algorithm for the analysis of 450K Illumina data showed that these changes were marked by de novo methylation. The same 4126 cytosines located in islands corresponding to 1059 genes were systematically methylated. This effect required cellular entry of the viral particle in the cells but not the genomic integration of the vector cassette. Some LV preparations induced only mild sporadic changes while others had strong effects suggesting that LV batch heterogeneity may be related to the extent of the epigenetic response.

Conclusion: These findings identify a previously uncharacterized but consistent cellular response to viral components and provide a novel example of environmentally modified epigenome.

No MeSH data available.


Related in: MedlinePlus

Venn diagram indicating the overlap between the eight different conditions identified as having “high” effect on increased methylation. 4126 is the number of CM-CpG sites. The different conditions were A dINT1b (76382 CpG-s); B dINTa (20337 CpG-s); C LV3a (29123 CpG-s); D LV3b (24818 CpG-s); E LV2 (29007 CpG-s); F dINT2 (57624 CpG-s); G dGEN2 (31059 CpG-s); H dGEN1b (20566 CpG-s), as defined on the Table 1
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Fig3: Venn diagram indicating the overlap between the eight different conditions identified as having “high” effect on increased methylation. 4126 is the number of CM-CpG sites. The different conditions were A dINT1b (76382 CpG-s); B dINTa (20337 CpG-s); C LV3a (29123 CpG-s); D LV3b (24818 CpG-s); E LV2 (29007 CpG-s); F dINT2 (57624 CpG-s); G dGEN2 (31059 CpG-s); H dGEN1b (20566 CpG-s), as defined on the Table 1

Mentions: To further characterize the DNA methylation changes, we compared the lists of CpG-s with increased and decreased methylation in the “high” and “low” clusters. The lists in the “low” cluster did not share common CpG-s. Similarly, the lists of CpG-s with decreased methylation did not overlap significantly with one another. By contrast, the comparison of the 8 lists of CpG-s with increased methylation obtained in the “high” group revealed a substantial overlap. The methylation of 4126 CpG sites became higher in all 8 conditions that involved different vector types (Fig. 3), but also CD34+ cells from different donors (Table 1). The probability to get such a high number of identical changes fortuitously is essentially zero (p < 10−60). These sites represent 7–20 % of all CpG-s with increased methylation that were detected in the various conditions and almost 1 % of all sites present on the Illumina array. This high number of recurrently de novo methylated CpG-s (commonly-modified CpG-s, CM-CpG) in a subset of genes suggests that the exposure of the cells to vector particles triggers the action of a common mechanism.Fig. 3


Systemic epigenetic response to recombinant lentiviral vectors independent of proviral integration.

Aranyi T, Stockholm D, Yao R, Poinsignon C, Wiart T, Corre G, Touleimat N, Tost J, Galy A, Paldi A - Epigenetics Chromatin (2016)

Venn diagram indicating the overlap between the eight different conditions identified as having “high” effect on increased methylation. 4126 is the number of CM-CpG sites. The different conditions were A dINT1b (76382 CpG-s); B dINTa (20337 CpG-s); C LV3a (29123 CpG-s); D LV3b (24818 CpG-s); E LV2 (29007 CpG-s); F dINT2 (57624 CpG-s); G dGEN2 (31059 CpG-s); H dGEN1b (20566 CpG-s), as defined on the Table 1
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4940770&req=5

Fig3: Venn diagram indicating the overlap between the eight different conditions identified as having “high” effect on increased methylation. 4126 is the number of CM-CpG sites. The different conditions were A dINT1b (76382 CpG-s); B dINTa (20337 CpG-s); C LV3a (29123 CpG-s); D LV3b (24818 CpG-s); E LV2 (29007 CpG-s); F dINT2 (57624 CpG-s); G dGEN2 (31059 CpG-s); H dGEN1b (20566 CpG-s), as defined on the Table 1
Mentions: To further characterize the DNA methylation changes, we compared the lists of CpG-s with increased and decreased methylation in the “high” and “low” clusters. The lists in the “low” cluster did not share common CpG-s. Similarly, the lists of CpG-s with decreased methylation did not overlap significantly with one another. By contrast, the comparison of the 8 lists of CpG-s with increased methylation obtained in the “high” group revealed a substantial overlap. The methylation of 4126 CpG sites became higher in all 8 conditions that involved different vector types (Fig. 3), but also CD34+ cells from different donors (Table 1). The probability to get such a high number of identical changes fortuitously is essentially zero (p < 10−60). These sites represent 7–20 % of all CpG-s with increased methylation that were detected in the various conditions and almost 1 % of all sites present on the Illumina array. This high number of recurrently de novo methylated CpG-s (commonly-modified CpG-s, CM-CpG) in a subset of genes suggests that the exposure of the cells to vector particles triggers the action of a common mechanism.Fig. 3

Bottom Line: The effects of LV on target cells are expected to be limited to gene delivery.This effect required cellular entry of the viral particle in the cells but not the genomic integration of the vector cassette.Some LV preparations induced only mild sporadic changes while others had strong effects suggesting that LV batch heterogeneity may be related to the extent of the epigenetic response.

View Article: PubMed Central - PubMed

Affiliation: Université Evry Val d'Essonne, UMRS_951, Genethon, 91002 Evry, France.

ABSTRACT

Background: Lentiviral vectors (LV) are widely used for various gene transfer or gene therapy applications. The effects of LV on target cells are expected to be limited to gene delivery. Yet, human hematopoietic CD34+ cells respond to functional LVs as well as several types of non-integrating LVs by genome-wide DNA methylation changes.

Results: A new algorithm for the analysis of 450K Illumina data showed that these changes were marked by de novo methylation. The same 4126 cytosines located in islands corresponding to 1059 genes were systematically methylated. This effect required cellular entry of the viral particle in the cells but not the genomic integration of the vector cassette. Some LV preparations induced only mild sporadic changes while others had strong effects suggesting that LV batch heterogeneity may be related to the extent of the epigenetic response.

Conclusion: These findings identify a previously uncharacterized but consistent cellular response to viral components and provide a novel example of environmentally modified epigenome.

No MeSH data available.


Related in: MedlinePlus