Single-cell multi-omic profiling of intratumoral heterogeneity to tackle oesophageal cancer cell adaptation to chemotherapy

Background.

Oesophageal cancer (OC) possesses a dismal clinical outcome and is the 7th most common cause of cancer deaths in the UK. Intratumoral heterogeneity (ITH) has been suggested as a major driver of drug resistance and cancer progression.

Previous studies failed to identify pre-existing resistant clones harbouring mutations in OC, which implies that non-genetic ITH might be a key driver of resistance.

Persister cells are drug-tolerant and can adapt to drug stress through a non-genetic mechanism, but they are genetically indistinguishable. However, these persisters have not been elucidated in OC. Aim.

In this fellowship, I aim to investigate the dynamic change of transcriptional and epigenetic ITH in OCs under chemotherapy at a single-cell level to identify drug-tolerant persisters and provide novel biomarkers to monitor and target those cells.

I also aim to establish a reproducible ex-vivo model to validate biomarkers and identify druggable targets for persisters. Methods.

To do this, I will perform state-of-art single-cell multi-omics in longitudinal clinical samples and establish a lineage-tracing platform in patient-derived organoids (PDOs).

I have established single-cell technologies, profiling single-cell transcriptomes and single-cell chromatin accessibility in serial biopsies of oesophago-gastric junctional adenocarcinoma under neoadjuvant chemotherapy.

The multi-omic analysis will elucidate how each cancer cell adapts to chemotherapy by non-genetic mechanism and delineate cell-type-specific responses to drugs. I will develop a novel single-cell pipeline to delineate transcriptional and epigenetic ITH. It will achieve the robust identification of novel biomarkers of persisters.

To validate the biomarkers, I will establish a lineage-tracing PDO platform with expressed barcodes, which are detectable by scRNA-seq.

This platform enables me to trace persisters under long-term drug stress and elucidate how cancer cells initially adapt to drugs and become fully resistant.

To identify novel therapeutic targets, I will also perform CRISPR/Cas9 screens with a custom pooled library in the PDO platform. Candidate genes will be further validated using CRISPR/Cas9 knock-out with individual sgRNAs in the PDO platform. How the results of this research will be used.

The fellowship will offer deeper insight into how transcriptional and epigenetic ITH affect drug response and provide novel biomarkers for monitoring and targeting persisters.

These biomarkers and therapeutic candidates will be offered in further clinical trials to investigate the clinical impact of persister-targeted therapy combined with chemotherapy in locally advanced oesophago-gastric adenocarcinoma.

The novel therapeutic strategy of cell type-specific treatment might benefit OCs patients to improve the dismal prognosis in OCs.