Recruitment of First-Time, Tenure-Track Faculty Members — Cancer Prevention and Research Institute of Texas

Grant Information

Grant ID	RR210034
Awarded On	May 19, 2021
Title	Recruitment of First-Time, Tenure-Track Faculty Members
Program	CPRIT Scholar
Award Mechanism	Recruitment of First-Time, Tenure-Track Faculty Members
Institution/Organization	The University of Texas Southwestern Medical Center
Principal Investigator/Program Director	Sihan Wu
Cancer Sites	Brain and Other Nervous System, Lung and Bronchus
Contracted Amount	$2,000,000
Summary of Goals and Objectives	Goal 1: Identify cancer cell lines that carry ecDNAs and generate genomic maps of ecDNAs in each line. Objectives: Reveal the ecDNA landscape of 329 cancer cell lines in the Cancer Cell Line Encyclopedia (CCLE) database by re-analyzing whole-genome sequencing (WGS) data and generating ecDNA reference maps containing genomic coordinates and gene annotations. Independently test the presence of ecDNAs in cell lines predicted to contain them by WGS and computational analysis. Validate ecDNA architecture by two-color FISH and generate 3D chromatin topology data by Hi-C. Goal 2: Characterize ecDNA replication. Objectives: Characte... Read More Goal 1: Identify cancer cell lines that carry ecDNAs and generate genomic maps of ecDNAs in each line Objectives: Reveal the ecDNA landscape of 329 cancer cell lines in the Cancer Cell Line Encyclopedia (CCLE) database by re-analyzing whole-genome sequencing (WGS) data and generating ecDNA reference maps containing genomic coordinates and gene annotations. Independently test the presence of ecDNAs in cell lines predicted to contain them by WGS and computational analysis. Validate ecDNA architecture by two-color FISH and generate 3D chromatin topology data by Hi-C. Goal 2: Characterize ecDNA replication Objectives: Characterize ecDNA replication features, including replication site, timing, domain organization, and synchronicity by high-resolution Repli-seq. Visualize ecDNA replication synchronicity by high-resolution confocal imaging. Identify DNA polymerase used for ecDNA replication by RNAi knockdown and confocal imaging. Goal 3: Model ecDNA formation in genetically engineered mice Objectives: Design and test sgRNA pairs targeting the Myc-Pvt1 chromosomal locus, deliver effective sgRNA pairs into Tp53-deficient mice with hepatic Cas9 expression and monitor development of hepatocellular carcinoma. Isolate hepatocellular carcinoma cells and characterize ecDNA particles by FISH and WGS to determine whether Myc is amplified. Use CRISPR-KO or RNAi to disrupt DNA polymerase genes in hepatocellular carcinoma cells to determine in vivo effects of loss of polymerase function(s) on ecDNA. Read Less