br Association of PTEN Deletion and ITH br
Association of PTEN Deletion and ITH
We also analyzed the association between ITH and mutational profiles, including somatic mutations and copy number alterations (CNAs), from whole-exome sequencing data. While most alterations did not showed any difference in degree of heterogeneity, there were substantial deviations in PTEN CNA (Figure 3A). To observe the genomic factors that can lead to a separation of clonality, information gain (IG) was adopted, and PTEN CNA among many factors showed
Translational Oncology Vol. 12, No. 1, 2019 Tumor Heterogeneity in Prostate Cancer Yun et al. 45
Figure 1. Heatmap of genomic alterations according to clonality. Landscape of somatic mutations with high frequency and copy number alterations from 85 prostate tumor samples (8 in 1 clone, 27 in 2 clones, 27 in 3 clones, and 23 in over 4 clones). When a tumor sample had one or two subclones, it was defined as an oligoclone; otherwise, the tumor was defined as a multiclone. Bar plot at the top represents PSA values (log10). Patient samples with a level greater than zero are highlighted in red.
the highest IG score. Other subsets such as PTEN mutation, ETV4 fusion, and SPOPL CNA also ranked high with regard to IG score but were not considered as important as PTEN CNA.
Tumors with wild type and those with PTEN Amphotericin showed considerable differences between high- and low-heterogeneity groups (P = .0027; Fisher's exact test) (Figure 3B). Interestingly, PCs with PTEN deletion possessed an overwhelmingly large proportion of multiclone tumors. Based on this result, we think that the PTEN deletion is one of the key markers associated with ITH.
We also analyzed the clonality among diploid, homozygous, and heterozygous PTEN deletion (Figure 3C). Our analysis revealed that multiclone PCs are notably enriched in heterozygous PTEN deletion compared to diploid or homozygous deletion (P = .001). In some
types of PCs, PTEN heterozygous and homozygous deletions have different characteristics such as Gleason score , and our study suggested different ITH patterns in the two studied groups. However, further clinical and biological investigation is warranted.
Functional Enrichment of Tumors with PTEN Deletion and ITH
PTEN CNA was positively correlated with mRNA expression (Figure 4A). As expected, the gene expression of genes with homozygous and heterozygous PTEN deletion was lower than that with diploid and gain. Moreover, we studied the kinds of genes differentially affecting clonality according to PTEN deletion. In order to identify genes associated with both PTEN deletion and clonality, we extracted DEGs for six possible combinations for PTEN deletion
Figure 2. Correlations between ITH and several factors in prostate cancer samples. (A) Bar plot of average PSA values according to number of clones. (B) Box plot of TMB according to number of clones. (C) Box plot of contribution scores of CD8 T-cell signature according to number of clones.
46 Tumor Heterogeneity in Prostate Cancer Yun et al. Translational Oncology Vol. 12, No. 1, 2019
Table 1. Demographic and Clinical Characteristics of Prostate Cancer Patients
Characteristic Oligoclone (n = 35) Multiclone (n = 50) P Value
Tumor cellularity (pathology)
(+ and −) and clonality (oligo and multi). Among them, only two combinations had significantly differentially expressed genes (Figure 4B). One was the test for PTEN Del (+) & multiclone vs. PTEN Del (−) & oligoclone. The other was the test for PTEN Del (+) & multiclone vs. PTEN Del (−) & multiclone. Several differently expressed genes such as PTEN, CDC42EP5, RNLS, GP2, NETO2, and AMPD3 were correlated with tumor heterogeneity in the presence of PTEN deletion (≥2-fold
change, adjusted P value b.05). In other words, high heterogeneity of a tumor with PTEN deletion may be dominantly driven by the expression of those genes.
According to previous studies, several pathways such as WNT, PI3CA, and androgen receptor signaling are known to regulate the progression of prostate cancer . Particularly, the PI3CA pathway was significantly affected by tumor heterogeneity (Figure 4, C and D). It is assumed that the altered PI3CA pathway is closely related to higher ITH with PTEN deletion.
In this study, we presented genomic and transcriptomic factors associated with the degree of ITH. Deletion of PTEN tumor suppressor gene occurs at high frequency in prostate cancer and is associated with clinical outcome and aggressive metastatic potential [16,17]. Although many studies regarding PTEN deletion in prostate cancer have been reported, the association with ITH has not been clarified. We demonstrated that it was frequently observed in tumors with high heterogeneity. It is still questionable whether the alteration of PTEN directly or indirectly causes tumor heterogeneity during prostate cancer progression.