Zhou, Binhua P.

Research Overview

Metastasis, the spread of cells from a primary tumor to distant sites, is the main cause of death in patients with pancreatic cancer. Epithelial-mesenchymal transition (EMT), a process vital for morphogenesis during embryonic development, is attracting increasing attention from oncologists as a potential mechanism for the initial step of metastasis. Many genes implicated in EMT during embryogenesis are being discovered, one after another, to control metastasis. We are currently focusing on the characterization of the functional role and regulation of Snail/Slug transcription factors in the control of EMT. Snail is a zinc-finger transcriptional repressor that was identified in Drosophila as a suppressor of the transcription of shotgun (an E-cadherin homologue) in the control of embryogenesis. Flies and mice without Snail are lethal because of severe defects at the gastrula stage during development. Expression of Snail correlates with the tumor grade and nodal metastasis of many types of tumor and predicts a poor outcome in patients with metastatic cancer, particularly pancreatic cancer.

In this project, we will study the genome interaction of Snail and transcription profile during EMT. We will employ lab-produced and public RNA- and ChIP-Seq datasets to uncover altered signaling pathways that regulate metastasis in cancer and, by discovery these pathways, to identify molecules that may serve as the therapeutic targets for metastasis prevention. Because of the size of the datasets of sequencing reads, we need use of HPC capacity.

Computational Method

Publicly available RNA- and ChIP-Seq data analyzing tools.

Software

This project will primarily rely on open-source software including:

Sambamba, VarScan, MuTect2, Samtools, Bedtools, HISAT2, STAR, Bowtie, Bowtie2, MISO, kallisto, HOMER, MACS2, featureCounts, among others. Some of these software will require additional dependencies, including Python, numpy, scipy, pysam, matplotlib libraries and R.

Personnel

PI - Peter Zhou,

Research Associate Senior - Zhibing Duan, Added 04/14/2021

Grants:

Publications: