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Histone modifier gene mutations in PTCL-NOS
groups, combined treatment led to significant modulation of multiple signaling pathways associated with cancer, including those of apoptosis, cell cycle progression, cell adhesion, and transcriptional regulation (Figure 5D). Particularly, PU.1 was included in both the cancer path- way and the transcriptional pathway in the combined treatment group. Pathway enrichment analysis of the overlapping genes of the RNA-Seq and ChIP-Seq in the combination group was then performed. Significant path- ways relevant to T-cell biology are shown in Figure 5E. As revealed by gene set enrichment analysis, the MAPK path- way was inactivated in the combination treatment group compared with the untreated group. Accordingly, p-ERK upregulation was observed not only in tumor samples of
PTCL-NOS patients with KMT2D mutations, but also in those of xenografted T-lymphoma mice bearing KMT2D V5486M mutants, the latter being inhibited by combined treatment with chidamide and decitabine (Figure 5F,G).
Discussion
First observed in B-cell lymphoma, recurrent mutations of epigenetic modifier genes have recently been identified in PTCL-NOS.9 In the present study, we performed target- ed sequencing of the main epigenetic modifier genes in a large cohort of Chinese PTCL-NOS patients. The results showed that the mutational spectrum of these genes in
ABC
DE
Figure 5. Chip-seq and RNA sequencing data of KMT2D-mutated T-lymphoma cells treated with chidamide and/or decitabine. (A) Venn diagram depicting the overlap between transcription factors bound by H3K4me3 ChIP-seq in the combination group, as compared to the chidamide (CHID)-treated group and the decitabine (DECI)- treated group in KMT2D V5486-mutated Jurkat cells. (B) The top significant transcription factors bound by H3K4me3 in the combination group. (C) ChIP-seq analysis of transcription factors bound by H3K4me3. Enriched H3K4me3-binding motifs for PU.1 analyzed by KMT2D V5486-mutated Jurkat cells treated with CHID and DECI rel- ative to genomic background (upper panel). Genomic snapshots of PU.1 peaks bound by H3K4me3 in different groups (lower panel). (D) Cellular and genetic information processing revealed by RNA-seq on the combination group in KMT2D V5486-mutated Jurkat cells. (E) Pathway analysis of the most differentially expressed genes that overlapped in both RNA-Seq and ChIP-Seq analysis in the combination group (upper panel). Gene-set enrichment analysis of the MAPK pathway (lower panel). (F) Immunohistochemical assay of p-ERK in tumor samples of PTCL-NOS patients with or without KMT2D mutations. (G) Immunostaining of p-ERK in tumor samples of xenografted murine models bearing KMT2D V5486 mutants treated with CHID and/or DECI. **P<0.01 compared with the untreated group. Bar=20 mm.
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