Table 2.

Overview of main changes identified in prostate cancer using different omics approaches.

Approach	Major Findings Early Stage	Major Findings Late Stage
Genomics	Low mutation rate High copy number and structural aberrations ETS-TMPRSS2 fusion PTEN deletion SPOP mutation FOXA1 mutation	AR amplification and mutation TP53 mutation RB1 deletion PIK3CA amplification
Epigenomics	Identification of DNA hypermethylation subtype associated with disease recurrence	Hypomethylation around AR gene Changes in H3K27 acetylation Changes in H3K9 di- and trimethylation Upregulation of lncRNA HOTAIR
Cistromics	AR cistrome rearrangement ETS factor-driven AR cistrome reprogramming Enrichment of FOXA1 and HOXB13 cistromes	Novel AR-V7 cistrome Changes in ZFX and SOX2 cistromes
Transcriptomics	Identification of subtypes predictive of recurrence and metastasis Changes linked to ETS fusion Changes linked to SPOP or FOXA1 mutation	Emergence of AR-V7 and other AR splice variants Expression upregulation of steroid synthesis genes
Proteomics	Ubiquitylome changes linked to SPOP mutation	Abundance of cell cycle and DNA damage response pathway proteins Role of FOXA1 and HOXB13 interactomes
Metabolomics	Changes in lipid and nucleotide metabolism Changes in TCA cycle, polyamine synthesis and hexoamine biosynthesis pathway