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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

Analysis of DNA methylation changes. Analyses of 4 different chip runs (a, b, c, d) testing a total of 12 different batches of vector annotated accordingly (i.e. dENV1a and dENV1b indicates a repeat testing of dENV1 batch on chip a and chip b). a Volcano plots of representative experiments. From left to right: methylation differences observed in cells infected with an integrative lentiviral vector showing a high effect (LV2), integrase-deficient particles (dINT2), genome-deficient (dGEN2) and envelope-deficient (dENV1) particles as compared to control cells cultured but without any vector. The last plot on the right represents a control triplicate compared to another control triplicate (as in bottom line of b). Each point on a volcano plot represents the maximal delta-β value of a CpG site in a given triplicate as a function of the median of the three delta-β values of that triplicate. Only the CpG-s identified as displaying altered methylation between the samples and their corresponding controls are shown. Points representing CpG sites with increased and decreased methylation are displayed on the right and left sites of the plot. Note the higher number of points and higher median and maximal delta-β values with increased methylation in the first three samples. b Hierarchical classification of the experimental conditions depending on the extent of the increase (left) or the decrease (right) of the genomic DNA methylation in CD34+ cells. The classification was done using the three parameters indicated in the table: number of changed CpGs (N), chi2 of genomic distribution and median delta-β
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Fig2: Analysis of DNA methylation changes. Analyses of 4 different chip runs (a, b, c, d) testing a total of 12 different batches of vector annotated accordingly (i.e. dENV1a and dENV1b indicates a repeat testing of dENV1 batch on chip a and chip b). a Volcano plots of representative experiments. From left to right: methylation differences observed in cells infected with an integrative lentiviral vector showing a high effect (LV2), integrase-deficient particles (dINT2), genome-deficient (dGEN2) and envelope-deficient (dENV1) particles as compared to control cells cultured but without any vector. The last plot on the right represents a control triplicate compared to another control triplicate (as in bottom line of b). Each point on a volcano plot represents the maximal delta-β value of a CpG site in a given triplicate as a function of the median of the three delta-β values of that triplicate. Only the CpG-s identified as displaying altered methylation between the samples and their corresponding controls are shown. Points representing CpG sites with increased and decreased methylation are displayed on the right and left sites of the plot. Note the higher number of points and higher median and maximal delta-β values with increased methylation in the first three samples. b Hierarchical classification of the experimental conditions depending on the extent of the increase (left) or the decrease (right) of the genomic DNA methylation in CD34+ cells. The classification was done using the three parameters indicated in the table: number of changed CpGs (N), chi2 of genomic distribution and median delta-β

Mentions: aSee Fig. 2b


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)

Analysis of DNA methylation changes. Analyses of 4 different chip runs (a, b, c, d) testing a total of 12 different batches of vector annotated accordingly (i.e. dENV1a and dENV1b indicates a repeat testing of dENV1 batch on chip a and chip b). a Volcano plots of representative experiments. From left to right: methylation differences observed in cells infected with an integrative lentiviral vector showing a high effect (LV2), integrase-deficient particles (dINT2), genome-deficient (dGEN2) and envelope-deficient (dENV1) particles as compared to control cells cultured but without any vector. The last plot on the right represents a control triplicate compared to another control triplicate (as in bottom line of b). Each point on a volcano plot represents the maximal delta-β value of a CpG site in a given triplicate as a function of the median of the three delta-β values of that triplicate. Only the CpG-s identified as displaying altered methylation between the samples and their corresponding controls are shown. Points representing CpG sites with increased and decreased methylation are displayed on the right and left sites of the plot. Note the higher number of points and higher median and maximal delta-β values with increased methylation in the first three samples. b Hierarchical classification of the experimental conditions depending on the extent of the increase (left) or the decrease (right) of the genomic DNA methylation in CD34+ cells. The classification was done using the three parameters indicated in the table: number of changed CpGs (N), chi2 of genomic distribution and median delta-β
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Analysis of DNA methylation changes. Analyses of 4 different chip runs (a, b, c, d) testing a total of 12 different batches of vector annotated accordingly (i.e. dENV1a and dENV1b indicates a repeat testing of dENV1 batch on chip a and chip b). a Volcano plots of representative experiments. From left to right: methylation differences observed in cells infected with an integrative lentiviral vector showing a high effect (LV2), integrase-deficient particles (dINT2), genome-deficient (dGEN2) and envelope-deficient (dENV1) particles as compared to control cells cultured but without any vector. The last plot on the right represents a control triplicate compared to another control triplicate (as in bottom line of b). Each point on a volcano plot represents the maximal delta-β value of a CpG site in a given triplicate as a function of the median of the three delta-β values of that triplicate. Only the CpG-s identified as displaying altered methylation between the samples and their corresponding controls are shown. Points representing CpG sites with increased and decreased methylation are displayed on the right and left sites of the plot. Note the higher number of points and higher median and maximal delta-β values with increased methylation in the first three samples. b Hierarchical classification of the experimental conditions depending on the extent of the increase (left) or the decrease (right) of the genomic DNA methylation in CD34+ cells. The classification was done using the three parameters indicated in the table: number of changed CpGs (N), chi2 of genomic distribution and median delta-β
Mentions: aSee Fig. 2b

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