Journal: Neoplasia (New York, N.Y.)
Article Title: Differential chromatin accessibility response to retinoic acid in neuroblastoma with ATRX in-frame-deletions versus ATRX loss-of-function
doi: 10.1016/j.neo.2025.101263
Figure Lengend Snippet: ATRX LoF neuroblastoma cells have an impaired chromatin response to RA compared to their wild-type counterparts. (A) Time course experiment showing expression of CYP26A , normalized to GAPDH following exposure of p53(2) ( ATRX wildtype) and E6 ( ATRX LoF) cells to retinoic acid (RA). Data represented as mean ± SEM of n = 3 ( t test, * P <0.05). (B) HOXA1 and HOXA4 expression by RT-qPCR following 72 hours treatment with RA, compared to vehicle control. Inverse log delta CT is indicated. Where no expression was seen, this is indicated as 0. Mean ± SEM of n = 3; t test, * P < 0.05. (C) Clonogenic assay results for p53(2) and E6 cell lines following treatment with 10μM RA versus control (mean ± SEM of n = 3; t test, *** P < 0.001). (D-E) Volcano plots showing differentially accessible regions in E6 versus p53(2) cell lines following (D) vehicle control treatment conditions and (E) RA treatment. (F) Venn diagrams comparing differentially accessible transcription factor binding motifs following RA treatment in p53(2) and E6 cell lines. (G-J) Gene ontology analysis, comparing differential accessibility at gene promoters between E6 and p53(2) lines in (G) vehicle control conditions and (H) following treatment with RA. Displayed terms have been selected using REVIGO which eliminates redundant GO terms. (I-J) List of pathways grouped under the term “regionalization” and “embryonic skeletal system development” by Revigo for (I) vehicle control and (J) RA treated samples, respectively.
Article Snippet: SH-SY5Y cells were subsequently electroporated with plasmids containing sgRNA for targeting Intron 1 and Intron 10 of ATRX as well as a pCE-mp53-DD plasmid (p53-DD) (Addgene Plasmid #41856) for transient inhibition of p53 [ , ] using the 4D-Nucleofector® X Unit with the SF Cell Line 4D-Nucleofector® X Kit L (Lonza, Cat# V4XC-2024), following the manufacturer’s protocol.
Techniques: Expressing, Quantitative RT-PCR, Control, Clonogenic Assay, Binding Assay
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