Fig. 1: KDM6B is marked with a highly active epigenetic landscape and highly expressed in neuroblastoma and regulates MYC expression. | Nature Communications

Fig. 1: KDM6B is marked with a highly active epigenetic landscape and highly expressed in neuroblastoma and regulates MYC expression.

From: KDM6B promotes activation of the oncogenic CDK4/6-pRB-E2F pathway by maintaining enhancer activity in MYCN-amplified neuroblastoma

Fig. 1

a–c The expression of KDM6B, KDM6A, and UTY in normal human trunk neural crest (GSE14340) and four different neuroblastoma cohorts (Versteeg GSE16476, Delattre GSE14880, Hiyama GSE16237, Lastowska GSE13136). y-Axis represents the normalized log2 expression value. n = 5 for NCC, n = 88 for Versteeg, n = 64 for Delattre, n = 51 for Hiyama, n = 30 for Lastowska. Data are represented as mean ± SD. ****p < 0.0001, two-tailed, unpaired t test. d–f The expression of KDM6B, KDM6A, and UTY in three different neuroblastoma RNA-seq cohorts. The RNA-seq data of St Jude (d) was downloaded from https://pecan.stjude.cloud. The RNA-seq data of TARGET (e) and SEQC (f) datasets were downloaded from R2 (https://hgserver1.amc.nl/cgi-bin/r2/main.cgi). y-Axis represents the Fragment Per Kilobase of transcript per Million (FPKM) mapped reads. n = 160 for St Jude dataset, n = 161 for TARGET dataset, n = 498 for SEQC dataset. Data are represented as mean ± SD. ****p < 0.0001, two-tailed, unpaired t test. g The epigenetic landscapes consisting of histone marks and transcription factor binding distinguish KDM6B from KDM6A in primary neuroblastoma tissues with MYCN amplification or without MYCN amplification (https://pecan.stjude.cloud/proteinpaint/study/mycn_nbl_2018). h Crystal violet staining of colonies after BE2C and SK-N-AS cells were transfected with four different siRNA oligos to knockdown KDM6B for 7 days. siCtrl = siRNA control oligo, NT = no treatment. i Western blot analysis with indicated antibodies to assess MYCN or C-MYC expression after 3-day transfection of 4 different siRNA to knockdown KDM6B in BE2C and SK-N-AS. The blots are representative of three independent experiments. j BE2C and MSCV-KDM6B overexpressing (KDM6B-OE) BE2C cells were transfected with siRNA control (siCtrl) and siRNA targeting the endogenous 3′ untranslated region (3′UTR) of KDM6B (siKDM6B-3′UTR). Four days later, cells were stained with crystal violet. k Quantification of cell density of each group (n = 3) using imageJ. Data are represented as mean ± SD. Shown are individual biological replicates. ****p < 0.0001, two-tailed, unpaired t test. l BE2C and MSCV-KDM6B overexpressing (KDM6B-OE) BE2C cells were transfected with siRNA control (siCtrl) and siRNA siKDM6B-3′UTR. Three days later, cells were subject to immunoblotting with indicated antibodies. The blots are representative of three independent experiments. Source data are provided as a “Source data” file.

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