Comprehensive characterisation of the FCGR locus using Oxford Nanopore sequencing to enhance immunotherapy efficacy | LC 25

Biography

Sarah Frampton works as a Postdoctoral Research Fellow in the Cancer Genomics Group at the University of Southampton. Her research focuses on leveraging long-read sequencing technologies to advance genomics research into the Fc gamma receptor locus, aiming to generate a comprehensive understanding of regulatory mechanisms that control Fc gamma receptor expression and enhance cancer immunotherapy efficacy.

Abstract

The success of monoclonal antibody immunotherapies has revolutionised cancer treatment; however, efficacy relies on the interaction with a family of proteins called the Fc gamma receptors (FcγR). The FCGR locus encodes both activating and inhibitory FcγRs whereby their expression ratio is associated with immunotherapy response and resistance. In addition to the 98% homologous segmental duplication, the FCGR locus is highly polymorphic, containing large copy number variants (CNVs) and numerous single nucleotide polymorphisms (SNPs). Historically, the locus has been extremely challenging to study, with standard short-read sequencing technologies failing to produce reads that can be adequately aligned or assembled. However, with Oxford Nanopore sequencing, the locus can now be accurately and comprehensively characterised for the first time.

Utilising a human cohort with diverse FCGR SNP and CNV profiles, Oxford Nanopore genomic and transcriptomic sequencing were deployed to uncover haplotype-resolved FCGR variants and examine transcript diversity across immune cells. Libraries were prepared from high-quality DNA and RNA extracted from human peripheral blood mononuclear cells (PBMCs) and sequenced on MinION and PromethION Flow Cells.

A pipeline designed for SNP and CNV detection, phasing, de novo assembly, and methylation profiling has advanced our understanding of FCGR genomic variation. This approach provided new insights into non-coding regulatory regions, identified novel chimeric genes, and uncovered important alternatively spliced transcripts.

Oxford Nanopore sequencing offers a groundbreaking solution to challenges posed by sequence homology, enabling the generation of comprehensive maps with phased sequences, breakpoints, and methylation data. This advancement enhances our understanding of FcγR regulation and opens pathways to manipulate their function for improved cancer patient outcomes.