Additional file 1 of Kidney cancer biomarkers and targets for therapeutics: survivin (BIRC5), XIAP, MCL-1, HIF1α, HIF2α, NRF2, MDM2, MDM4, p53, KRAS and AKT in renal cell carcinoma
Creators: name: Li, Fengzhi
name: Aljahdali, Ieman A. M.
name: Zhang, Renyuan
name: Nastiuk, Kent L.
name: Krolewski, John J.
name: Ling, Xiang
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Hematology

description: Additional file 1: Supplemental Material 1. Role of NRF2 in non-cancerous disease prevention and aging retardation. Supplemental Table S1. Summary of the datasets collected from publicly available kidney tumor tissues versus normal tissue samples*. Supplemental Table S2. Somatic Mutation Analysis Summary of relevant genes*. Supplemental Table S3. Classification of KIRP/pRCC tumor and normal tissues into Type 1 pRCC and Type 2 pRCC. Supplemental Figure S1. NRF2 expression in Type 1 pRCC and Type 2 pRCC tumor tissues versus in normal renal tissues: Boxplots of the NRF2 expression level across TCGA Type 1 or Type 2 pRCC tumor tissues (red) versus the normal renal tissues (blue) were presented (A). NRF2 expression among different stages of Type 1 pRCC tumor tissues versus the matched normal tissue (B) or versus all normal tissues (C) was box-plotted. NRF2 expression among different stages of Type 2 pRCC tumor tissues versus matched normal tissue was box-plotted (D). NRF2 expression was presented in the log2 (TPM + 1) scale format. Data was presented as the mean ± standard deviation (SD). A t-test was used to evaluate the statistical significance of the NRF2 mRNA expression level in renal normal tissues versus either Type 1 or type 2 pRCC tumor tissues. One-way ANOVA was used to compare NRF2 expression among renal normal tissues versus different stages of Type 1 or Type 2 pRCC tumor tissues. The figure was performed using R version 4.0.3. Supplemental Figure S2. Effects of NRF2 expression on Type 1 pRCC patient survival probability: Kaplan-Meier survival analyses of overall survival (OS) from TCGA-Type 1 (A) or Type 2 (B) pRCC cohorts were presented. Patients were grouped into the high NRF2 expression group versus the low NRF2 expression group based on the median NRF2 mRNA expression level in either Type 1 (A) or Type 2 (B) pRCC tumor tissues. Each p-value for the significance from high versus low NRF2 expression was calculated using the log-rank test. The figures were performed using R version 4.0.3. Supplemental Figure S3. Mdm4/MdmX expression in RCC tumor tissues versus in normal tissues: Boxplots of the Mdm4MdmX expression level across TCGA-RCC subtypes in renal tumor (red) versus the associated normal renal tissues (blue) were presented (A). Mdm4MdmX expression among different stages of chRCC (B), ccRCC (C) and pRCC (D) versus normal renal tissues was box-plotted. Mdm4MdmX expression was presented in the log2 (TPM + 1) scale format. Data was presented as the mean ± SD. A t-test was used to evaluate the statistical significance of the mRNA expression level in renal normal versus tumor tissues. One-way ANOVA was used to compare Mdm4MdmX expression among renal normal tissues versus different stages of RCC tumor tissues. The figure was performed using R version 4.0.3. Supplemental Figure S4. Effects of Mdm4/MdmX expression on RCC patient survival probability: Kaplan-Meier survival analyses of OS from TCGA-RCC cohorts of ccRCC (A), chRCC (B) and pRCC(C) were presented. Patients were grouped into the high Mdm4/MdmX expression group versus the low Mdm4/MdmX expression group based on the median Mdm4/MdmX mRNA expression. Each p-value for the significance from high versus low Mdm4/MdmX expression was calculated using the log-rank test. The figures were performed using R version 4.0.3. Supplemental Figure S5. AKT2 expression in RCC tumor tissues versus in normal tissues: Boxplots of the AKT2 expression level across TCGA-RCC subtypes in renal tumor (red) versus the associated normal renal tissues (blue) were presented (A). AKT2 expression among different stages of chRCC (B), ccRCC (C) and pRCC (D) versus normal renal tissues was box-plotted. AKT2 expression was presented in the log2 (TPM + 1) scale format. Data was presented as the mean ± SD. A t-test was used to evaluate the statistical significance of the mRNA expression level in renal normal versus tumor tissues. One-way ANOVA was used to compare AKT2 expression among renal normal tissues versus different stages of RCC tumor tissues. The figure was performed using R version 4.0.3. Supplemental Figure S6. Effects of AKT2 expression on RCC patient survival probability: Kaplan-Meier survival analyses of OS from TCGA-RCC cohorts of ccRCC (A), chRCC (B) and pRCC (C) were presented. Patients were grouped into the high AKT2 expression group versus the low AKT2 expression group based on the median AKT2 mRNA expression. Each p-value for the significance from high versus low AKT2 expression was calculated using the log-rank test. The figures were performed using R version 4.0.3.