# Pan-Cancer Analyses Reveal Genomic Features of FOXM1 Overexpression in Cancer
## 2 Results
### FOXM1 Overexpression in Pan-Cancer Correlates with TP53 and RB1 Alterations  
Recently, _TP53_ mutations, Rb-E2F deregulation, and _FOXM1_ amplification or expression were found to be enriched in high aneuploidy breast tumors [43]. Prior in vitro studies have also linked _TP53_ and _RB1_ loss to increased FOXM1 expression [44; 25; 45; 46]. Therefore, we used UCSC Xena Browser Heat Maps to visualize the relationship between _FOXM1_ mRNA expression, _FOXM1_ copy number, _TP53_ mutations, _RB1_ copy number, and FOXM1 target gene expression across all TCGA primary tumors. Notably, TCGA primary tumors with high _FOXM1_ expression demonstrated more frequent _TP53_ mutations, _RB1_ copy number loss, and activation of FOXM1 target genes (Figure 4A). Additionally, tumors with intermediate _FOXM1_ expression but _FOXM1_ diploid or copy number loss tended to have _TP53_ mutations and _RB1_ loss, while tumors with low _FOXM1_ expression displayed _FOXM1_ diploid or copy number loss, wild-type _TP53_, and diploid _RB1_ (Figure 4A). To formally test these associations, we grouped TCGA primary tumors by _TP53_ and _RB1_ status and compared FOXM1 mRNA and protein expression levels. We observed the highest FOXM1 mRNA and protein expression in tumors with alterations in both _TP53_ and _RB1_, with either single alteration giving an intermediate phenotype (Figure 4B,C). These data implicate p53 and Rb-E2F deregulation as key drivers of FOXM1 overexpression in pan-cancer. Figure 3: Association of FOXM1 expression with aneuploidy in TCGA pan-cancer. (**A**) _FOXM1_ mRNA expression (RNA-seq RSEM, log2(norm count +1)) correlations with tumor aneuploidy scores in TCGA primary tumors. (**B**) FOXM1 protein expression (RPPA, pan-can normalized) correlation with tumor aneuploidy score in TCGA primary tumors. (**C**) _FOXM1_ mRNA expression (RNA-seq RSEM, log2(norm count +1)) correlation with tumor aneuploidy score in _FOXM1_ diploid TCGA primary tumors. (**D**) FOXM1 protein expression (RPPA, pan-can normalized) correlations with tumor aneuploidy scores in _FOXM1_ diploid TCGA primary tumors. High-Grade Serous Ovarian Cancer (HGSC) and Basal Breast Cancer (BBC) Have Highly Similar FOXMI Alterations  
TCGA reported that HGSC and BBC show similar genomic features, including ubiquitous _TP53_ mutations and increased genomic instability in the form of copy number alterations, as compared to other subtypes of breast cancer and other cancer types [6,47]. We hypothesized that basal breast cancer (BBC) may show similar FOXM1 alterations to HGSC. However, in TCGA pan-cancer data, breast cancer (BRCA) showed a lower frequency of FOXM1 mRNA, protein expression, and genomic amplifications compared to HGSC (Figure 1A,B; Figure 2A). Because TCGA BRCA data do not  
Figure 4: FOXM1 expression in TCGA cancer types by p53/Rb status. (**A**) Comparison of _FOXM1_ mRNA expression, _FOXM1_ copy number, _TP53_ somatic mutations, _RB1_ copy number, and FOXM1 target genes among all TCGA primary tumors with overlapping genomics data. Data were retrieved from UCSC Xena. FOXM1 target genes included _AURKB_, _CCNA2_, _CCNB1_, _CCNB2_ and _CENPA_. (**B**,**C**) FOXM1 expression in tumors with _T53_ somatic mutations and _RB1_ copy number loss. (**B**) _FOXM1_ mRNA expression (RNA-seq RSEM, log2(norm count +1)) in tumors with _T53_ somatic mutations (\(n\) = 1288), _RB1_ copy number loss or somatic mutation (\(n\) = 190), both alterations (\(n\) = 128) or neither alteration (\(n\) = 3362). (**C**) FOXM1 protein expression (RPPA pan-can normalized) in tumors with _T53_ somatic mutations (\(n\) = 1288), _RB1_ copy number loss or somatic mutation (\(n\) = 190), both alterations (\(n\) = 128), or neither alteration (\(n\) = 3362). Mann-Whitney test \(p\) values are shown. \(p\) value designations: **** \(<\) 0.0001, ** \(<\) 0.01,  
differentiate between breast cancer subtypes, we retrieved TCGA PAM50 expression subtype data for TCGA breast cancer and categorized samples based on molecular subtype.