br Previous studies have reported that
Previous studies have reported that most PTEN deletions of primary tumors were concordantly found in metastatic sites [5,6,18]. It is highly possible that PTEN deletions are early occurring mutations as they tend to be observed in multiple lesions. A study on ERG rearrangements and PTEN deletions in prostate cancer indicated that they are early events during tumor progression . That prior study has reported that PTEN heterozygous deletions showed higher frequency than homozygous deletions in diverse tissues obtained from benign prostate tissue to high-grade prostatic intraepithelial neoplasia and prostate cancer. In our study, both types
Figure 3. PTEN deletion as an indicator of tumor heterogeneity in prostate cancer. (A) Contribution score of genomic and transcriptomic features. Information gain for each feature was measured between oligo- and multiclonal samples. (B) Comparison of clonality between tumor samples with PTEN deletion and those with wild type. (C) Comparison of clonality among diploid, homozygous, and heterozygous PTEN deletion.
Translational Oncology Vol. 12, No. 1, 2019 Tumor Heterogeneity in Prostate Cancer Yun et al. 47
Figure 4. Gene expression and function associated with PTEN deletion and tumor heterogeneity. (A) Correlation between PTEN deletion and corresponding gene expression. Expression values are the log-transformed normalized read counts. (B) The result of DEG analysis for six possible combinations for PTEN deletion (+ and −) and clonality (oligo and multi). DEGs were found in only two tests: 1) PTEN Del (+)
& multiclone vs. PTEN Del (−) & oligoclone, 2) PTEN Del (+) & multiclone vs. PTEN Del (−) & multiclone. (C) Enriched pathways associated with PTEN deletion and tumor heterogeneity. This result was obtained from gene set enrichment analysis for PTEN Del (+) & multiclone vs. PTEN Del (−) & oligoclone. (D) Enrichment of genes involved in the PI3K cascade pathway.
showed similar frequency and increased ITH. However, ITH was higher in heterozygous deletions than in homozygous.
A number of studies have suggested that tumor infiltrating immune Meropenem can accelerate tumor invasion and metastasis [19–22]. However, the most recent study has demonstrated that progressing metastases showed the characterization of immune cell exclusion, while repressing and stable metastases exhibited infiltration of CD8+ T cells in ovarian cancers . In our study, the activation score of CD8-positive T cell or cytotoxic T cell was negatively correlated with ITH, indicating that the pattern observed from our analysis is consistent with the characteristics of cancer progression. The heterogeneity of clones can vary depending on the immune-microenvironment of the surrounding tumor in prostate cancer.
We demonstrated that the expression of several genes was significantly associated with ITH potentially via PTEN deletion. These genes were PTEN, CDC42EP5, RNLS, GP2, NETO2, and AMPD3. Overexpression of Neuropilin and tolloid-like 2 (NETO2) has been found in many cancer types including proliferating hemangiomas and colorectal carcinoma [24–26] and thus could be considered as a potential biomarker in tumor progression. Recent study have suggested that adenosine monophosphate deaminase 3 (AMPD3) deletion suppresses the proliferation, migration, and invasion of gastrointestinal stromal tumor . AMPD3 expression is positively correlated with ERG overexpression and PTEN inactivation in prostate cancer
[28,29]. This result suggests that this abnormal alteration is tightly correlated with tumor heterogeneity and may be useful in the development of prognostic markers or novel drug targets in prostate cancer.
In conclusion, progression of ITH could foster tumor evolution in association with PTEN deletion, which is one of the key mechanisms in prostate cancer progression. Genes identified from ITH analysis could potentially serve as a biomarker promoting ITH or a therapeutic target.
Conflicts of Interest
Conflict of interest relevant to this article was not reported.
The study was supported in part by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1D1A1B03034779).
48 Tumor Heterogeneity in Prostate Cancer Yun et al. Translational Oncology Vol. 12, No. 1, 2019
 Furusato B, Gao CL, Ravindranath L, Chen Y, Cullen J, McLeod DG, Dobi A, Srivastava S, Petrovics G, and Sesterhenn IA (2008). Mapping of TMPRSS2-ERG fusions in the context of multi-focal prostate cancer. Mod Pathol 21, 67–75.
 Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, and Camacho N, et al (2015). Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet 47, 367–372.