Date: Wednesday, 5 May 2021

Venue: Cheung Kung Hai Lecture Theatre 2, G/F, William M.W. Mong Block, Faculty of Medicine Building, 21 Sassoon Road, Pokfulam, Hong Kong [Mixed mode: Face-to-Face and Zoom]

Time: 5:00 p.m. - 6:00 p.m.

Zoom Link: https://hku.zoom.us/j/97048450898?pwd=S2xRME9UTnZ0TGZlVFBRT0pQSzlXQT09

Meeting ID: 970 4845 0898

Password: 119002

Time: 5:00 p.m.
Speaker: Dr. Jayne Barbour (Post-doctoral Fellow)
Primary Supervisor: Dr. JWH Wong
Presentation Title: Mutations in CTCF-cohesin Binding Sites in Cancer
Abstract: Mutations acquired in cancer genomes form distinct patterns. CTCF-cohesin binding sites (CBS), or DNA loop anchors, and are vulnerable to accumulating mutations. To explore why CBS are vulnerable to mutagenesis we performed analysis of somatic mutation densities in CBS on 1980 whole-genome sequenced cancer samples. We found three groups of samples with enriched CBS mutations densities: skin, gastrointestinal and XPD mutant bladder cancers. XPD is a DNA helicase that is part of TFIIH and mutated in ~10% of bladder cancer. XPD mutant samples displayed elevated mutation densities in accessible chromatin and at transcriptionally active CBS. In a separate project we tested if a germline mutation in a specific CBS in the CDKN2B locus is important in melanoma. Dermal fibroblasts from a family of sporadic melanoma harbouring this variant were cultured and we performed CTCF ChIP-seq, HiC and RNA-seq. We observed allele-specific loss of CTCF binding suggesting the variant is functional.

Time: 5:30 p.m. 
Speaker: Dr. Ken Hung-On Yu (Assistant Research Officer)
Primary Supervisor: Dr. JWK Ho
Presentation Title: Scalable detection of microbial transcripts in human single cells
Abstract: Single cell RNA-sequencing (scRNA-seq) has enabled the study of gene expression in individual cells and corresponding cell types. The most widely used scRNA-seq technology today, 10x Genomics Chromium, allows analysing tens of thousands to millions of single cells together. Many studies have characterised viruses in human single cell samples, such as SARS-CoV-2 in COVID-19 patient samples. However, there are few general approaches for the detection of all types of viruses or microbes with potential host interaction in 10x scRNA-seq; therefore, we created one with scalability and robustness as main considerations. Our pipeline is easy to use, involves a reference set of all known human host viruses and microbes, aims to utilise cloud computing, has options to use any state-of-the-art method, and is tailored for discovering viruses and microbes in single cell data. We benchmark scalability of state-of-the-art methods on real data, their sensitivity and specificity on simulated data, and demonstrate a use case of discovering previously undetected H. Pylori in public pre-gastric cancer clinical scRNA-seq data.

ALL ARE WELCOME

Should you have any enquiries, please feel free to contact Miss River Wong at 3917 9216.