Mechanisms of gene regulation in cancer

University Of Pennsylvania, Philadelphia PA

Investigators

Abstract

ABSTRACT This proposal provides salary support for a highly productive Research Specialist, Dr. Charly Good, working in the lab of a well-established Unit Director, Dr. Shelley Berger. This proposed work is an integral part of Dr. Berger's NCI funded cancer research program, which focuses on understanding how wildtype (WT) and gainof- function (GOF) mutant p53 sculpt the genome for gene regulation. p53 is a transcriptional activator that directly binds DNA to induce tumor suppressor gene expression. Dr. Berger's group has made seminal discoveries in how p53 functions in cancer, including the groundbreaking discovery that select hotspot mutations in p53 (GOF p53) confers oncogenic abilities through activation of key epigenetic pathways. Understanding how GOF p53 regulates its target genes is a major question that, after exhaustive study, still remains unanswered. Enhancer clusters (ECs) are groups of enhancers that cluster together in 3D space to drive high levels of gene expression. Dr. Good is currently addressing the following questions. 1) what proteins interact with GOF p53 to drive cancer growth? 2) does GOF p53 reorganize ECs to drive high levels of gene expression? 3) what transcription factor(s) does GOF p53 collaborate with to rewire ECs? 4) what target genes does GOF p53 regulate via rewiring of ECs? P53 also regulates genes by bringing them close to nuclear speckles (NS) to boost expression. Dr. Good is mentoring trainees in the lab to 5) identify which GOF p53 target genes associate with NS and test the function of this regulation and 6) identify how p53 associates with NS by identifying the proteins that interact with the praline rich domain of p53. Dr. Good will be responsible for: (1) generating the high-throughput HiChlP, RNA-seq, and Poree datasets in cancer cells with WT and GOF p53 mutations; (2) analyzing the sequencing data to identify how normal WT p53 functions at ECs and importantly, how GOF p53 rewires ECs to promote cancer growth; (3) performing molecular biology experiments and cancer assays to test the functional consequences of disrupting critical ECs and nuclear speckle association using CRISPR gene editing approaches. This work will be viewed with a translational lens, whereby all genomics data will be analyzed in a way that offers clinically relevant insights to improve upon patient therapy. Dr. Good is also involved in the ongoing T cell work in the Unit Director's lab, publishing several first-author papers on T cell exhaustion in cancer and mentoring trainees in this area. Dr. Good has worked with Dr. Berger since 2017. Together, they have published numerous high-quality manuscripts and have advanced our understanding of cancer biology. Dr. Good is a key resource in Dr. Berger's laboratory, where she directly mentors graduate students and postdocs and teaches both wet and dry lab techniques to trainees. The Research Specialist award would be a tremendous opportunity for Dr. Good and would support her career development as a staff scientist. She will be instrumental in advancing the robust cancer research program in Dr. Berger's laboratory and will help to train the next generation of scientists.