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. 2021 May;18(5):1332-1335.
doi: 10.1038/s41423-020-0518-4. Epub 2020 Aug 20.

DNA methylation profile of a hepatosplenic gamma/delta T-cell lymphoma patient associated with response to interferon-α therapy

Jaydeep Bhat  1   2 , Anke K Bergmann  3   4 , Silvio Waschina  5   6 , Christoph Nerl  7 , Christoph Kaleta  5 , Reiner Siebert  3   8 , Ole Ammerpohl  9   10 , Dieter Kabelitz  11
Affiliations

DNA methylation profile of a hepatosplenic gamma/delta T-cell lymphoma patient associated with response to interferon-α therapy

Jaydeep Bhat et al. Cell Mol Immunol. 2021 May.
No abstract available

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
DNA methylation analysis of the γδ-HSTL patient during IFNα2c therapy. DNA methylation analysis was performed on bisulfite-converted DNA from PBMCs of the γδ-HSTL patient obtained at five different time points during continued IFNα2c therapy. a The violin plot represents the distribution of the methylation of 273 statistically significant CpG loci at different visits, including the quartiles and median methylation. The DNA methylation level was calculated using the average β-value of the respective CpG site. Only for statistical purposes was the adjusted p value calculated for visits 1 and 5 using the paired Wilcoxon test. The statistical significance is shown as *** for p values ≤ 0.005. b The heatmap was plotted after normalization to the mean methylation level (average β-value) of CpG sites, as indicated by scales in the color key. c The heatmap presents Pearson’s correlation values from visit 1 to visit 5. The range of correlation values is shown in the color key at the top-left side of the plot. d The principal component analysis (PCA) plot of significant CpG loci (similar to the violin plot) represents the separation of two different components depending on the DNA methylome during the visits of the γδ-HSTL patient. e The functional gene ontology (GO) analysis of genes related to the CpG loci from visits 1 to 5. The GO terms enriched in categories, namely, biological process (left-side), cellular component (right-side top), molecular function (right-side middle), and KEGG pathway (right-side lower), are presented for criteria of statistical significance p value ≤ 0.05. f The cosine similarity score was calculated as described in the Supplementary material. Cosine similarity between the DNA methylation of healthy T cells and cells from the γδ-HSTL patient at visits (1–5) during IFNα2c therapy. The statistical significance of p values ≤ 0.05 is represented as *** for the difference between visit 1 and healthy T cells. g As shown in Table S1 and represented in Supplementary Fig. 4B, flow cytometry analysis of PBMCs in γδ-HSTL patient visits during IFNα2c therapy was performed. Based on forward scatter (FSC) and sideward scatter (SSC), lymphocytes and non–lymphocytes were gated within the PBMCs. The data are represented as the percentage gated with a statistically significant difference for p values ≤ 0.05, ≤0.01, and ≤0.005 shown as ***, **, and *, respectively
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References

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