Additional file 1 of The feedback loop of EFTUD2/c-MYC impedes chemotherapeutic efficacy by enhancing EFTUD2 transcription and stabilizing c-MYC protein in colorectal cancer
Creators: name: Zhu, Xiaojian
name: Li, Changxue
name: Gao, Yunfei
name: Zhang, Qingyuan
name: Wang, Tao
name: Zhou, Huaixiang
name: Bu, Fanqin
name: Chen, Jia
name: Mao, Xinjun
name: He, Yulong
name: Wu, Kaiming
name: Li, Ningning
name: Luo, Hongliang
Publisher: name: figshare
Year: 2024
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology
subject: Computational Biology

description: Additional file 1: Fig. S1. EFTUD2 is significantly upregulated in 5-FU chemotherapy-resistant cells of CRC, related to Fig. 1. A Analysis of the differential expression genes (DEGs) expression in 5-FU resistant CRC cell lines compared with parental cell lines using three GEO datasets (GSE166900, GSE81005, GSE81008). B Analysis of 18 significantly upregulated genes shared among CRC chemoresistant cells using Venn diagram. C Multivariate Cox regression analysis of 18 candidate genes and identification of top four genes (EFTUD2, VIM, EFNB2, and PLAC1) using TCGA. D Analysis of EFTUD2 expression in the non-responsive group compared with response group to FOLFOX and FOLFIRI using CTRP. E GSEA using the gene set linked to EFTUD2 in CRC from TCGA. **P &lt; 0.01. Fig. S2. High EFTUD2 expression is a potential independent predictor of poor prognosis in CRC, related to Fig. 2. A Analysis of EFTUD2 in predicting survival probability in CRC patients based on Cox regression analysis using Nomogram-related model. B Calibration curve analysis depicting the differentiation between predicted and actual survival rates of the model at different time points (1-year, 2-year, and 3-year). Fig. S3. EFTUD2 attenuates the chemotherapy efficacy of 5-FU in vitro, related to Fig. 3. A MTT assay showing the influence of various concentrations of 5-FU on viability of SW480, HCT116, and Caco-2 cells. B Clone formation and EdU assays showing the influence of EFTUD2 upregulation on cell survival and proliferation in SW480 cells treated with 5-FU. C and D TUNEL apoptosis assays showing the influence of EFTUD2 modulation on apoptosis in SW480, HCT116, and Caco-2 cells treated with 5-FU. Each bar represents the mean values ± SD, *P &lt; 0.05; **P &lt; 0.01; ***P &lt; 0.001. Fig. S4. Correlation and expression analysis of EFTUD2 with candidate genes, related to Fig. 5. A Heat map showing the top five genes correlated with EFTUD2 in CRC using TCGA. B-F Differentiation expression analysis showing the mRNA expression levels of MYC, PRPF8, WBP4, SF3A2, and SNRNP40 in CRC tissues compared with adjacent normal tissues using TCGA. ***P &lt; 0.001. Fig. S5. MYC promotes the transcription of EFTUD2, related to Fig. 7. A GSEA showing the transcription factors related to EFTUD2 in CRC using TCGA. B ChIP-seq analysis of MYC binding peaks on EFTUD2 using Cistrome Data Browser. Fig. S6. Correlation and overall survival analysis of EFTUD2 with 17 significantly upregulated genes shared in CRC chemoresistant cells. A Heat map showing the correlation between EFTUD2 and 17 significantly upregulated genes using the TCGA. B Kaplan-Meier analysis of overall survival in two groups of CRC patients stratified by high and low expression of top three genes (SLC2A1, L1CAM, and IL32) using TCGA. Fig. S7. Overexpressing EFTUD2 promotes the epithelial-mesenchymal transition (EMT) phenotype. A and B Analysis of EMT markers (Vimentin, E-cadherin, ZEB1, and Slug) after overexpressing EFTUD2 in SW480 and HCT116 cells using RT-qPCR. Each bar represents the mean values ± SD, *P &lt; 0.05; **P &lt; 0.01; ****P &lt; 0.0001. Supplementary Table 1. Correlation analyses of EFTUD2 with sensitivity to common chemotherapeutic drugs in CRC. Supplementary Table 2. Correlation analyses between EFTUD2 expression and clinicopathological characteristics of CRC patients using TCGA. Supplementary Table 3. The sequence of primers used in Fig.7K and Fig. 8