Research: Splicing · Gene regulation · Cancer

How isoforms shape cancer.

Genes are often described as the functional units of the genome, but this is a convenient abstraction. In reality, genes are modular collections of sequences that are assembled in myriad ways to produce distinct isoforms. In cancer, RNA processing goes awry, leading to widespread misexpression of isoforms. In our lab, we develop and apply high-throughput genomic approaches to address the question: how do isoforms contribute to cancer, and can they be exploited as diagnostics and therapeutics? We pursue three connected themes, and focus on breast cancer, the most common cancer in women worldwide.
normaltumorisoform Aisoform B
1

How do TF isoforms rewire gene regulatory networks?

Isoforms of transcription factors (TFs) are highly diverse in their biochemical and molecular functions. But what effect do TF isoforms have on gene regulation in cancer cells? We screen TF isoforms in models of healthy mammary cells and breast cancer subtypes, linking isoform-specific perturbations to phenotypic read-outs and following up on individual isoforms mechanistically. The goal is to determine, causally, how individual TF isoforms reshape gene expression programs and oncogenic cell states.

Techniques: ORF libraries · Cas13d · Perturb-seq · CUT&RUN / RNA-seq

2

How does splicing change throughout drug treatment?

Drug resistance is a persistent challenge in breast cancer. We study how alternative splicing and related processes become rewired in cancer cells over time as they are exposed to both cytotoxic and targeted drugs using in vitro models. The goal is to further understand mechanisms of drug resistance and to, hopefully, find ways in which aberrant splicing can be exploited as a potential vulnerability in drug-resistant cells.

Techniques: Long-read RNA-seq · Single-cell RNA-seq · DNA-seq / ATAC-seq

t₀tᵒ
3

Can we develop better ways to perturb isoforms?

Current tools limit how precisely we can perturb individual isoforms. We are engineering new approaches to do high-throughput isoform perturbations, including improved RNA-targeting CRISPR/Cas systems, more principled guide RNA design models, and cleaner isoform over-expression approaches. We believe that better tools will enable us to move further “beyond the gene”.

Techniques: Cas13d · Perturb-seq · ORF libraries · [insert your idea here!]