Cancer

Integration of a large cohort of transcriptome, whole genome, and ATAC-sequencing characterizes the chromatin accessibility changes in advanced prostate cancer and identifies therapy-resistant prostate cancer subtype-specific transcription factors that modulate oncogenic programs.

We discovered a group of metastatic prostate cancer patients with lower levels of DNA-DNA interactions around the Androgen Receptor (AR) gene, the main driver of prostate cancer. Interestingly, this group had an abundance of circular DNA outside of the chromosomes (extrachromosomal circular DNA (ecDNA)) that included parts of the AR gene resulting in AR gene amplification and become very active, which might explain why their cancer was resistant to treatment.

Biomarkers of HPV-negative head and neck cancer

LGSOC is a rare tumor subtype with high case fatality rates in patients with metastatic disease. Here, we use multiomics integration of whole-exome sequencing, RNA sequencing, and mass spectrometry–based proteomics on LGSOC cell lines to elucidate novel biomarkers and therapeutic vulnerabilities.