Analysis of enhancer activity changes in late-stage prostate cancer

Prostate cancer is one of the most common cancer types in Turkish men. At nearly all stages of the disease, the androgen receptor (AR) is the main driver of initiation and growth. When activated, the AR binds to enhancer cis-regulatory elements and induces gene expression through chromatin loops that connect enhancers with target promoters. Given its critical function, targeting AR activity is the standard of care to treat metastatic or recurrent prostate cancer. While treatment is initially effective, resistance inevitably occurs. Yet even in these resistant tumors, AR remains the critical driver of proliferation in the vast majority of patients. There is increasing evidence that alterations to enhancer regulatory elements, either through cistrome reprogramming or somatic mutations, can act as acquired drivers of resistance. While both chromatin looping and AR's transcription factor function play an important role in enhancer activity, the extent of their contribution is not fully understood. In this work, we hypothesize that resistance in late-stage prostate cancer is driven by alterations in enhancer activity. Enhancer activity can be influenced by both changes in transcription factor activity and alterations in enhancer-promoter interactions. To investigate the changes in transcription factor activity, we functionally characterized the enhancer activity of a constitutively active AR splice variant using a massively parallel reporter assay. Unexpectedly we found that ARv7, a variant linked with resistance in clinical disease, repressed enhancer activity of AR. Next, we integrated the chromatin looping data from models of distinct stages of prostate cancer and identified significant changes in enhancer- promoter interactions in later stages of the disease. We detected new enhancer-promoter interactions in the late-stage model that are absent in the early-stage counterpart. This suggests that new chromatin interactions can change enhancer activity and may potentially contribute to resistance in late-stage prostate cancer. These results highlight the complex interplay between AR and chromatin organization, shedding light on novel mechanisms driving late-stage prostate cancer.