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. 2022 Oct 29;13:6457. doi: 10.1038/s41467-022-34179-8

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Global transcriptome changes associated with THZ531 (500 nM) treatment for 6 h in Colo829 (left) and A375 (right) cells. b Correlation between THZ531-induced gene expression changes in Colo829 and A375 cells. Displayed r = 0.703 value was determined using Pearson correlation. c Global THZ531-induced transcriptome changes (Colo829 and A375). d Correlation between THZ531-induced transcriptome changes in cells (A375 and Colo829) and gene length. Linear regression for significant perturbed genes is displayed (Slope −0.3297, p-value <0.0001). e Gene length of significant up- and downregulated genes by THZ531 treatment (A375, Colo829). f Number of genes up- or downregulated relative to gene length. The genome was ranked from smaller to longer genes and fractioned into 10 groups containing the same number of genes. g GSEA analysis revealed that the KEGG_HOMOLOGOUS_RECOMBINATION gene set is decreased in both THZ531-treated cells. Immunoblot of Colo829 cells treated for 12 h (h) or 24 h (i) with increasing concentrations of THZ531. j, k GSEA analysis revealed that the TNFA_SIGNALING_VIA_NFKB and PID_AP_PATHWAY gene sets are positively enriched in both THZ531-treated A375 and Colo829 cells. l qPCR of Colo829 cells treated for 6 h with THZ531. m Enrichment of the number of genes according to their length for the indicated GSEA term. The genome was ranked from smaller to longer genes and fractioned into 5 groups containing the same number of genes. Data are represented as mean of n = 3 independent biological replicates for each cell line (a, b, g, j, k) and n = 6 (A375 and Colo829) (c, d, f). Length of deregulated genes from n = 3 independent biological replicates for each cell line (e). For panels (a–f) Log₂ FC (THZ531/Control) above 1 or below −1 (twofold) and P-values ≤ 0.05 were respectively considered as significantly upregulated (red) or downregulated (blue). (h, i) Representative data of independents n = 3. Data are represented as mean ± SD of independent experiment, n = 3 (l). Significance was determined using Wald test (c), or unpaired two-tailed Student’s t-tests (e, l). Source data are provided as a Source Data file.