RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy

Abstract

RRM2B plays a crucial role in DNA replication, repair and oxidative stress. While germline RRM2B mutations have been implicated in mitochondrial disorders, its relevance to cancer has not been established. Here, using TCGA studies, we investigated RRM2B alterations in cancer. We found that RRM2B is highly amplified in multiple tumor types, particularly in MYC-amplified tumors, and is associated with increased RRM2B mRNA expression. We also observed that the chromosomal region 8q22.3-8q24, is amplified in multiple tumors, and includes RRM2B, MYC along with several other cancer-associated genes. An analysis of genes within this 8q-amplicon showed that cancers that have both RRM2B-amplified along with MYC have a distinct pattern of amplification compared to cancers that are unaltered or those that have amplifications in RRM2B or MYC only. Investigation of curated biological interactions revealed that gene products of the amplified 8q22.3-8q24 region have important roles in DNA repair, DNA damage response, oxygen sensing, and apoptosis pathways and interact functionally. Notably, RRM2B-amplified cancers are characterized by mutation signatures of defective DNA repair and oxidative stress, and at least RRM2B-amplified breast cancers are associated with poor clinical outcome. These data suggest alterations in RR2MB and possibly the interacting 8q-proteins could have a profound effect on regulatory pathways such as DNA repair and cellular survival, highlighting therapeutic opportunities in these cancers.

Keywords: 8q-amplicon; MYC; RRM2B; cancer; chromosome 8.

FIGURE 1

Somatic alterations in RRM2B from cbioportal.org. (A) Somatic alterations in RRM2B across TCGA studies. BLCA, Bladder urothelial carcinoma; BRCA, Breast invasive carcinoma; CESC, Cervical squamous cell carcinoma and endocervical adenocarcinoma; COAD, Colon adenocarcinoma; SKCM, Skin cutaneous melanoma; USEC, Uterine corpus endometrial carcinoma; ESCA, Esophageal carcinoma; TGCT, Testicular germ cell tumors; HNSC, Head and neck squamous cell carcinoma; LIHC, Liver hepatocellular carcinoma; MESO, Mesothelioma; NHL, Non-Hodgkin lymphoma; LUAD, Lung adenocarcinoma; OV, Ovarian serous cystadenocarcinoma; PAAD, Pancreatic adenocarcinoma; PCPG, Pheochromocytoma and paraganglioma; PRAD, Prostate adenocarcinoma; KIRC, Kidney renal clear cell carcinoma; SARC, Sarcoma. Amplifications (gray), mutations (green), and deletions (pink) are represented as percent frequency. (B) RRM2B mutations in TCGA. 2D RRM2B protein stick figure showing the important domains of RRM2B [N-terminal swivel region, required for dimer stability, gray; ribonucleotide small subunit signature (conserved region in catalytic site between RRM2 and RRM2B), blue, and iron-binding residues required for catalytic activity, red] and the number of somatic mutations in RRM2B. (C) Frequency of TP53, MYC, RRM1, RRM2 and RRM2B alterations in ovarian (OC), breast (BC), and head and neck (HNSCC) cases.

FIGURE 2

Amplification frequency of 8q-genes in ovarian cancer (OC). (A) cases with co-amplification of RRM2B and MYC; (B) cases MYC only amplification; (C) cases RRM2B only amplifications; (D) cases with neither (unaltered) were plotted as percent of frequency for amplifications in various 8q-region genes relevant for cancer (see Supplementary Table 1). RRM2B (red circle), MYC (yellow circle), and other genes (blue circle). The Pearson correlation (R² value) for the data points is represented by a black trend line.

FIGURE 3

Amplification frequency of cancer relevant 8q-genes in SKCM, Skin cutaneous melanoma; PAAD, Pancreatic adenocarcinoma; OC, Ovarian serous cystadenocarcinoma; HNSCC, Head and neck squamous cell carcinoma; LIHC, Liver hepatocellular carcinoma; CESC, Cervical and endocervical cancers; ESCA, Esophageal carcinoma; BC, Breast invasive carcinoma; STAD, Stomach adenocarcinoma; LUAD, Lung adenocarcinoma; COAD, Colon adenocarcinoma; BLCA, Bladder urothelial carcinoma, amplifications were plotted as percent of frequency for amplifications. RRM2B (red circle), MYC (yellow circle), and other genes (blue circle). The Pearson correlation (R² value) for the data points is represented by a black trend line.

FIGURE 4

An interactive network of RRM2B and related genes. The network represents proteins that functionally interact or intersect with RRM2B (yellow) or other 8q-gene products (purple). Red lines represent direct interaction, and green lines—physical association (interactions classified according to the BioGRID database annotation).

FIGURE 5

Mutation signature in breast cancer (BC) cases segregated by amplification type. One-way ANOVA (RRM2B amplifications only vs. other groups) and two-way ANOVA (included group with RRM2B and MYC co-amplifications) analysis showed that the T > C and T > G mutations are statistically significant. Top panels: tumor whole-exome sequence data from the PanCancer Atlas studies was used to calculate the average frequency of the 96 trinucleotide context mutations in each group: unaltered cases, cases with only RRM2B amplifications, cases with only MYC amplifications, and cases with amplifications in both. Bottom panels: The statistical significance of each comparisons is represented by ANOVA tests as -log10 (P-value) for each of the 96 trinucleotide context mutations. The -log10 (P) visualizations are provided for: one-way ANOVA comparing RRM2B only group to all other groups, a two-way ANOVA comparing all groups with RRM2B or MYC amplifications. -log10 (P)—the taller the bars are, the lower is the P-value and when the bars exceed the red line, P-values are less than 5%. P-values of each subfigure have been corrected using Benjamini–Hochberg procedure.

FIGURE 6

Kaplan-Meier curves for OS and DFS in breast cancer (BC) (A,B) and its subtypes (C–G) studies with RRM2B amplifications and/or MYC amplifications. (A) OS in BC cases. The cases that were unaltered for both genes (black, n = 737), cases with RRM2B amplifications (red, n = 14), cases with MYC amplifications (blue, n = 62) and co-amplifications (pink, n = 210) were plotted. (B) DFS in BC cases. The cases that were unaltered for both genes (black, n = 678), cases with RRM2B amplifications (red, n = 12), cases with MYC amplifications (blue, n = 55) and co-amplifications (pink, n = 184) were plotted. (C) OS in ER + PR + HER2 + BC cases. The cases that were unaltered for RRM2B (black, n = 68), cases with RRM2B amplifications (salmon, n = 18). (D) DFS in ER + PR + HER2 + cases. The cases that were unaltered for RRM2B (black, n = 63), cases with RRM2B amplifications (red, n = 13). (E) OS in BC subtypes with RRM2B amplifications. ER + PR + HER2 + cases with amplifications in RRM2B (purple, n = 18), ER- PR- HER2- cases with amplifications in RRM2B (blue, n = 26), and ER + PR + HER2- cases with amplifications in RRM2B (peach, n = 36). (F) DFS in BC subtypes with RRM2B amplifications. ER + PR + HER2 + cases with amplifications in RRM2B (purple, n = 13), ER- PR- HER2- cases with amplifications in RRM2B (blue, n = 25), and ER + PR + HER2- cases with amplifications in RRM2B (peach, n = 34). The plots were compared using Log-rank test and significance is shown as follows: *P < 0.05, **P < 0.01, and ***P < 0.001. (G) P-values for the graphs (E,F).