Genome-wide chromatin structure and function in Kaposi Sarcoma tissue

Barnard College, New York NY

Investigators

Abstract

Project Summary/Abstract The Kaposi sarcoma-associated herpesvirus (KSHV) is an etiological agent of cancer. Among these malignancies, Kaposi sarcoma (KS) is particularly prevalent in people living with HIV. Central to identifying potential points of therapeutic intervention is a fundamental understanding of how the virus drives cancer progression at the molecular level. Since its discovery decades ago, the field has excelled at laboratory studies of KSHV infection. Particular challenges remain, however, in studying actual tissue. This proposal attempts to bridge this gap with a focused project that connects key collaborators in the greatest areas of need. By building on established relationships with a biorepository and leveraging resources at an advanced core facility, this project aims to study hard-to-find specimens with frontline genomics methods. All experiments will be performed by undergraduate students. Specific Aim 1 will identify virus-associated host enhancers and regulated genes in KS tissue. The project will obtain clinical specimens of KS from the AIDS and Cancer Specimen Resource. Skin lesions will be brought to and processed at the Mount Sinai School of Medicine Center for Advanced Genomics Technology for multiome single-cell ATAC-seq and single-cell RNA-seq experiments. The sequencing data of open chromatin and gene expression will be analyzed by a team of undergraduates from Barnard College. The goal is to identify enhancers and regulated genes modulated by the presence of viral infection. This will provide a map of chromatin interactions from actual cancer tissue and represents a transformative step beyond cell culture studies. Specific Aim 2 will identify host super-enhancers in KS tissue. To complement the open chromatin experiments of Aim 1, Aim 2 will use ChIP-seq to identify super-enhancers for KS. The same frozen tumor tissue from the AIDS and Cancer Specimen Resource in Aim 1 will be processed. ChIP-seq will be performed using antibodies against BRD4, a host regulator of super- enhancer activity. The goal is to identify active super-enhancers. This will provide a map of key oncogene regulatory elements from actual cancer tissue and represents a transformative step beyond cell culture studies. The AREA Impact Strategy emphasizes student peer mentorship and leadership. This proposal will designate three students to serve as laboratory mentors and leaders. Along with the principal investigator, the peer leaders will coordinate experiments and data analysis with other students on the team. This intertwines mentorship training with the research experience and provides opportunities at multiple levels of engagement. The overall impact will be identification of potential drivers of KS. Elucidating regulatory architecture and circuitry will identify enhancers and transcription factors that may be essential for growth and potential targets in future treatments.