Single-cell multiomics profiling in the study of colorectal cancer evolution

Ogbeidi Igbinoba, Silvia Uhunoma (2024) Single-cell multiomics profiling in the study of colorectal cancer evolution. Doctoral thesis, University of East Anglia.

Preview

PDF Download (16MB) | Preview

Abstract

Colorectal cancer (CRC) remains a significant global health concern, with metastatic CRC (mCRC) presenting particularly poor prognoses due to the high failure rate of existing treatments, including targeted therapies. The emergence of drug resistance severely undermines the efficacy of these therapies, highlighting the urgent need for new approaches to overcome or prevent resistance to improve patient outcomes.

This study aimed to investigate the characteristics of mCRC patient-derived organoids (PDOs) in response to two AKT inhibitors (AKTi): MK-2206 and AZD5363/capivasertib. The primary focus was on characterising the PDOs after they developed resistance to these inhibitors, with the goal of uncovering resistance mechanisms at both transcriptional and genomic levels. To achieve this, single-cell genome and transcriptome sequencing (G&T-seq) was applied to MK2206-resistant, AZD5363-resistant, and control mCRC organoids. This method allowed for extensive profiling of mCRC cells, and provided valuable insights into the relationship between genomic alterations and their effects on the transcriptome of resistant cells.

Using this single-cell multiomics approach, the research identified genes potentially associated with resistance to AKT inhibition, implicating various processes such as energy metabolism, extracellular matrix remodelling, and immune response regulation. A key finding was the expansion of a pre-existing resistant subclone, characterised by specific copy number alterations (CNAs) on chromosomes (chr) 2 and 5, in both AKTi-resistant organoids. This suggests a potential drug-agnostic resistance mechanism, with the same subclone being selected for under different selective pressures. Furthermore, a direct correlation between CNAs on chr2 and chr5 and gene expression was evident in MK-2206-resistant cells. However, this correlation was not consistently observed for chr5 in AZD5363-resistant cells, suggesting that compensatory mechanisms could have modulated gene dosage effects in this organoid.

By integrating genomic and transcriptomic datasets, researchers can identify altered genes at the DNA level and correlate these changes with gene expression patterns that drive malignant processes. This approach underscores the importance of considering both molecular layers to fully understand cancer evolution and inform the development of new treatments.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Kitty Laine
Date Deposited:	12 Nov 2024 13:56
Last Modified:	12 Nov 2024 13:56
URI:	https://ueaeprints.uea.ac.uk/id/eprint/97647
DOI:

Downloads

Actions (login required)

View Item