Deciphering Cancer Heterogeneity and Drug resistance using Single-Clone Genomic and Epigenomic Landscapes

Introduction

To comprehend the characteristics, phylogenetic relationships, and drug resistance of tumor subclones, measurements must be performed at single-cell or single-clone resolution.

Aims of the Project

Aim 1 and Aim 2

Aims 1 and 2 aim to create cost-effective and reliable single-cell drop technologies for capturing:

• Full-length RNA (Scfl-RNA-Seq)
• Enhancers at the DNA level (ChromOpen)

It is noteworthy that Scfl-RNA-Seq also captures non-coding and non-polyadenylated RNAs besides coding mRNA. ChromOpen also offers better capturing of functional enhancers and higher sensitivity compared to the conventional technology.

Aim 3

The ultimate goal of Aim 3 is to create the first technology that can capture both full-length RNA and enhancers from the same cell (Multi-Omics). To increase sensitivity and coverage, Multi-Omics will be combined with a 3D-culturing system (3Dclone) that facilitates the growth of primary cancer cells into small clones.

The single-clone based Multi-Omics maps will:

1. Increase the discovery rate of genetic somatic diversity, including non-coding regions.
2. Reveal connections between gene expression and mutated loci.
3. Display a wider range of functional state associations between cells.

Aim 4

In Aim 4, using our innovative mapping technologies, we will investigate two brain tumors:

• Non-Small Cell Lung Cancer that has spread to the brain
• Glioblastoma primary cells

Both of these cancers have limited treatment options and poor outcomes due to drug resistance. Based on temporal drug treatment experiments and advanced mapping technologies, this data will improve our understanding of somatic driver mutations and cellular diversity in the context of resistance, and ultimately, lead to the identification of new therapeutic targets.